PDB Short entry for 3TPP HEADER HYDROLASE/HYDROLASE INHIBITOR 08-SEP-11 3TPP TITLE CRYSTAL STRUCTURE OF BACE1 COMPLEXED WITH AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 43-454; COMPND 5 SYNONYM: ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID COMPND 6 PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, COMPND 7 MEMAPSIN-2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; COMPND 8 EC: 3.4.23.46; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BACE, BACE1, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MEMAPSIN 2, PROTEASE, BACE1, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.XU,M.J.LI,H.GREENBLATT,T.T.CHEN,I.SILMAN,J.L.SUSSMAN REVDAT 3 08-NOV-17 3TPP 1 REMARK REVDAT 2 13-JUN-12 3TPP 1 JRNL REVDAT 1 23-NOV-11 3TPP 0 JRNL AUTH Y.C.XU,M.J.LI,H.GREENBLATT,W.Y.CHEN,A.PAZ,O.DYM,Y.PELEG, JRNL AUTH 2 T.T.CHEN,X.SHEN,J.H.HE,H.L.JIANG,I.SILMAN,J.L.SUSSMAN JRNL TITL FLEXIBILITY OF THE FLAP IN THE ACTIVE SITE OF BACE1 AS JRNL TITL 2 REVEALED BY CRYSTAL STRUCTURES AND MOLECULAR DYNAMICS JRNL TITL 3 SIMULATIONS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 13 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 22194329 JRNL DOI 10.1107/S0907444911047251 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 67220 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3408 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.1820 - 4.6095 1.00 2884 145 0.1874 0.1729 REMARK 3 2 4.6095 - 3.6593 1.00 2750 157 0.1314 0.1511 REMARK 3 3 3.6593 - 3.1969 1.00 2736 137 0.1515 0.1702 REMARK 3 4 3.1969 - 2.9047 1.00 2747 133 0.1715 0.2027 REMARK 3 5 2.9047 - 2.6966 1.00 2710 145 0.1757 0.2105 REMARK 3 6 2.6966 - 2.5376 1.00 2690 158 0.1610 0.1917 REMARK 3 7 2.5376 - 2.4105 1.00 2682 150 0.1585 0.1888 REMARK 3 8 2.4105 - 2.3056 1.00 2708 130 0.1531 0.2003 REMARK 3 9 2.3056 - 2.2168 1.00 2694 133 0.1403 0.2076 REMARK 3 10 2.2168 - 2.1403 1.00 2702 143 0.1374 0.1441 REMARK 3 11 2.1403 - 2.0734 1.00 2667 139 0.1360 0.1712 REMARK 3 12 2.0734 - 2.0142 1.00 2686 132 0.1340 0.1592 REMARK 3 13 2.0142 - 1.9611 1.00 2714 131 0.1267 0.1659 REMARK 3 14 1.9611 - 1.9133 1.00 2667 139 0.1342 0.1881 REMARK 3 15 1.9133 - 1.8698 1.00 2684 146 0.1321 0.1833 REMARK 3 16 1.8698 - 1.8300 1.00 2666 149 0.1306 0.1635 REMARK 3 17 1.8300 - 1.7934 1.00 2639 169 0.1330 0.1684 REMARK 3 18 1.7934 - 1.7595 1.00 2656 150 0.1421 0.1745 REMARK 3 19 1.7595 - 1.7281 1.00 2679 137 0.1520 0.1855 REMARK 3 20 1.7281 - 1.6988 0.99 2665 132 0.1599 0.1846 REMARK 3 21 1.6988 - 1.6714 0.98 2605 146 0.1685 0.1818 REMARK 3 22 1.6714 - 1.6457 0.96 2554 135 0.1856 0.2197 REMARK 3 23 1.6457 - 1.6215 0.91 2392 151 0.1979 0.2398 REMARK 3 24 1.6215 - 1.5987 0.84 2235 121 0.2254 0.2282 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 44.59 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63540 REMARK 3 B22 (A**2) : 0.85410 REMARK 3 B33 (A**2) : -0.21880 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.028 3173 REMARK 3 ANGLE : 2.319 4330 REMARK 3 CHIRALITY : 0.227 473 REMARK 3 PLANARITY : 0.013 563 REMARK 3 DIHEDRAL : 13.092 1135 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3TPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68069 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 81.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.910 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2QP8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5-1.8M LI2SO4, 100MM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.26750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.26750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 52.27400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.10100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 52.27400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.10100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.26750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 52.27400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.10100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.26750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 52.27400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.10100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -39 REMARK 465 GLY A -38 REMARK 465 SER A -37 REMARK 465 SER A -36 REMARK 465 HIS A -35 REMARK 465 HIS A -34 REMARK 465 HIS A -33 REMARK 465 HIS A -32 REMARK 465 HIS A -31 REMARK 465 HIS A -30 REMARK 465 SER A -29 REMARK 465 ALA A -28 REMARK 465 GLY A -27 REMARK 465 GLU A -26 REMARK 465 ASN A -25 REMARK 465 LEU A -24 REMARK 465 TYR A -23 REMARK 465 PHE A -22 REMARK 465 GLN A -21 REMARK 465 GLY A -20 REMARK 465 THR A -19 REMARK 465 LEU A -18 REMARK 465 PRO A -17 REMARK 465 ARG A -16 REMARK 465 GLU A -15 REMARK 465 THR A -14 REMARK 465 ASP A -13 REMARK 465 GLU A -12 REMARK 465 GLU A -11 REMARK 465 PRO A -10 REMARK 465 GLU A -9 REMARK 465 GLU A -8 REMARK 465 PRO A -7 REMARK 465 GLY A -6 REMARK 465 ARG A -5 REMARK 465 GLY A 158 REMARK 465 PHE A 159 REMARK 465 PRO A 160 REMARK 465 LEU A 161 REMARK 465 ASN A 162 REMARK 465 GLN A 163 REMARK 465 SER A 164 REMARK 465 GLU A 165 REMARK 465 VAL A 166 REMARK 465 LEU A 167 REMARK 465 ALA A 168 REMARK 465 SER A 169 REMARK 465 ASP A 311 REMARK 465 VAL A 312 REMARK 465 ALA A 313 REMARK 465 ILE A 386 REMARK 465 PRO A 387 REMARK 465 GLN A 388 REMARK 465 THR A 389 REMARK 465 ASP A 390 REMARK 465 GLU A 391 REMARK 465 SER A 392 REMARK 465 THR A 393 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A -4 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 7 CZ NH1 NH2 REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 SER A 10 OG REMARK 470 ARG A 128 CZ NH1 NH2 REMARK 470 LYS A 142 CD CE NZ REMARK 470 ARG A 205 NH1 REMARK 470 LYS A 214 NZ REMARK 470 LYS A 256 CD CE NZ REMARK 470 GLN A 271 OE1 NE2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 GLN A 316 CG CD OE1 NE2 REMARK 470 GLU A 364 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 731 O HOH A 731 3655 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 104 CD GLU A 104 OE2 0.085 REMARK 500 ARG A 195 CG ARG A 195 CD -0.204 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 61 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 PHE A 108 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 130 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 195 NE - CZ - NH1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 366 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 108 -64.53 -108.12 REMARK 500 ASN A 114 -0.39 75.10 REMARK 500 ASN A 114 -1.55 76.39 REMARK 500 TRP A 197 -85.50 -145.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 197 TYR A 198 149.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5HA A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 394 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 414 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TPJ RELATED DB: PDB REMARK 900 RELATED ID: 3TPL RELATED DB: PDB REMARK 900 RELATED ID: 3TPR RELATED DB: PDB DBREF 3TPP A -18 393 UNP P56817 BACE1_HUMAN 43 454 SEQADV 3TPP MET A -39 UNP P56817 EXPRESSION TAG SEQADV 3TPP GLY A -38 UNP P56817 EXPRESSION TAG SEQADV 3TPP SER A -37 UNP P56817 EXPRESSION TAG SEQADV 3TPP SER A -36 UNP P56817 EXPRESSION TAG SEQADV 3TPP HIS A -35 UNP P56817 EXPRESSION TAG SEQADV 3TPP HIS A -34 UNP P56817 EXPRESSION TAG SEQADV 3TPP HIS A -33 UNP P56817 EXPRESSION TAG SEQADV 3TPP HIS A -32 UNP P56817 EXPRESSION TAG SEQADV 3TPP HIS A -31 UNP P56817 EXPRESSION TAG SEQADV 3TPP HIS A -30 UNP P56817 EXPRESSION TAG SEQADV 3TPP SER A -29 UNP P56817 EXPRESSION TAG SEQADV 3TPP ALA A -28 UNP P56817 EXPRESSION TAG SEQADV 3TPP GLY A -27 UNP P56817 EXPRESSION TAG SEQADV 3TPP GLU A -26 UNP P56817 EXPRESSION TAG SEQADV 3TPP ASN A -25 UNP P56817 EXPRESSION TAG SEQADV 3TPP LEU A -24 UNP P56817 EXPRESSION TAG SEQADV 3TPP TYR A -23 UNP P56817 EXPRESSION TAG SEQADV 3TPP PHE A -22 UNP P56817 EXPRESSION TAG SEQADV 3TPP GLN A -21 UNP P56817 EXPRESSION TAG SEQADV 3TPP GLY A -20 UNP P56817 EXPRESSION TAG SEQADV 3TPP THR A -19 UNP P56817 EXPRESSION TAG SEQADV 3TPP ALA A 75 UNP P56817 LYS 136 ENGINEERED MUTATION SEQADV 3TPP ALA A 77 UNP P56817 GLU 138 ENGINEERED MUTATION SEQRES 1 A 433 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER ALA GLY SEQRES 2 A 433 GLU ASN LEU TYR PHE GLN GLY THR LEU PRO ARG GLU THR SEQRES 3 A 433 ASP GLU GLU PRO GLU GLU PRO GLY ARG ARG GLY SER PHE SEQRES 4 A 433 VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER GLY GLN SEQRES 5 A 433 GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO PRO GLN SEQRES 6 A 433 THR LEU ASN ILE LEU VAL ASP THR GLY SER SER ASN PHE SEQRES 7 A 433 ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS ARG TYR SEQRES 8 A 433 TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP LEU ARG SEQRES 9 A 433 LYS GLY VAL TYR VAL PRO TYR THR GLN GLY ALA TRP ALA SEQRES 10 A 433 GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO HIS GLY SEQRES 11 A 433 PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA ILE THR SEQRES 12 A 433 GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN TRP GLU SEQRES 13 A 433 GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA ARG PRO SEQRES 14 A 433 ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU VAL LYS SEQRES 15 A 433 GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN LEU CYS SEQRES 16 A 433 GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL LEU ALA SEQRES 17 A 433 SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE ASP HIS SEQRES 18 A 433 SER LEU TYR THR GLY SER LEU TRP TYR THR PRO ILE ARG SEQRES 19 A 433 ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG VAL GLU SEQRES 20 A 433 ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS GLU TYR SEQRES 21 A 433 ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR THR ASN SEQRES 22 A 433 LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA VAL LYS SEQRES 23 A 433 SER ILE LYS ALA ALA SER SER THR GLU LYS PHE PRO ASP SEQRES 24 A 433 GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP GLN ALA SEQRES 25 A 433 GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SER LEU SEQRES 26 A 433 TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE ARG ILE SEQRES 27 A 433 THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL GLU ASP SEQRES 28 A 433 VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE ALA ILE SEQRES 29 A 433 SER GLN SER SER THR GLY THR VAL MET GLY ALA VAL ILE SEQRES 30 A 433 MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA ARG LYS SEQRES 31 A 433 ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL HIS ASP SEQRES 32 A 433 GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE VAL THR SEQRES 33 A 433 LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO GLN THR SEQRES 34 A 433 ASP GLU SER THR HET 5HA A 999 41 HET CL A 394 1 HET CL A 395 1 HET CL A 396 1 HET CL A 397 1 HET CL A 398 1 HET CL A 399 1 HET CL A 400 1 HET CL A 401 1 HET URE A 402 4 HET URE A 403 4 HET URE A 404 4 HET URE A 405 4 HET URE A 406 4 HET URE A 407 4 HET URE A 408 4 HET URE A 409 4 HET URE A 410 4 HET URE A 411 4 HET URE A 412 4 HET SO4 A 413 5 HET SO4 A 414 5 HETNAM 5HA N-[(1S,2R)-1-BENZYL-3-(CYCLOPROPYLAMINO)-2- HETNAM 2 5HA HYDROXYPROPYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'- HETNAM 3 5HA [(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE HETNAM CL CHLORIDE ION HETNAM URE UREA HETNAM SO4 SULFATE ION FORMUL 2 5HA C31 H38 N4 O5 S FORMUL 3 CL 8(CL 1-) FORMUL 11 URE 11(C H4 N2 O) FORMUL 22 SO4 2(O4 S 2-) FORMUL 24 HOH *331(H2 O) HELIX 1 1 PHE A -1 VAL A 3 5 5 HELIX 2 2 GLN A 53 SER A 57 5 5 HELIX 3 3 TYR A 123 ALA A 127 5 5 HELIX 4 4 PRO A 135 THR A 144 1 10 HELIX 5 5 ASP A 180 SER A 182 5 3 HELIX 6 6 ASP A 216 ASN A 221 1 6 HELIX 7 7 LYS A 238 SER A 252 1 15 HELIX 8 8 PRO A 258 LEU A 263 1 6 HELIX 9 9 PRO A 276 PHE A 280 5 5 HELIX 10 10 LEU A 301 TYR A 305 1 5 HELIX 11 11 GLY A 334 GLU A 339 1 6 HELIX 12 12 ASP A 378 CYS A 382 5 5 SHEET 1 A 9 ARG A 61 PRO A 70 0 SHEET 2 A 9 ALA A 75 SER A 86 -1 O LEU A 80 N LYS A 65 SHEET 3 A 9 TYR A 15 VAL A 20 -1 N THR A 19 O SER A 86 SHEET 4 A 9 LEU A 6 ARG A 7 -1 N ARG A 7 O TYR A 15 SHEET 5 A 9 GLY A 171 ILE A 176 -1 O GLY A 172 N LEU A 6 SHEET 6 A 9 PHE A 150 CYS A 155 -1 N GLN A 153 O SER A 173 SHEET 7 A 9 PHE A 341 ASP A 346 -1 O PHE A 345 N PHE A 150 SHEET 8 A 9 ARG A 351 SER A 357 -1 O ALA A 355 N TYR A 342 SHEET 9 A 9 TYR A 184 PRO A 192 -1 N THR A 191 O ILE A 352 SHEET 1 B13 ARG A 61 PRO A 70 0 SHEET 2 B13 ALA A 75 SER A 86 -1 O LEU A 80 N LYS A 65 SHEET 3 B13 VAL A 95 ASP A 106 -1 O ALA A 101 N GLU A 79 SHEET 4 B13 PHE A 38 GLY A 41 1 N VAL A 40 O ILE A 102 SHEET 5 B13 GLY A 117 GLY A 120 -1 O ILE A 118 N ALA A 39 SHEET 6 B13 GLN A 25 ASP A 32 1 N LEU A 30 O LEU A 119 SHEET 7 B13 TYR A 15 VAL A 20 -1 N VAL A 20 O GLN A 25 SHEET 8 B13 LEU A 6 ARG A 7 -1 N ARG A 7 O TYR A 15 SHEET 9 B13 GLY A 171 ILE A 176 -1 O GLY A 172 N LEU A 6 SHEET 10 B13 PHE A 150 CYS A 155 -1 N GLN A 153 O SER A 173 SHEET 11 B13 PHE A 341 ASP A 346 -1 O PHE A 345 N PHE A 150 SHEET 12 B13 ARG A 351 SER A 357 -1 O ALA A 355 N TYR A 342 SHEET 13 B13 TYR A 184 PRO A 192 -1 N THR A 191 O ILE A 352 SHEET 1 C 5 GLU A 200 VAL A 201 0 SHEET 2 C 5 SER A 225 VAL A 227 -1 O SER A 225 N VAL A 201 SHEET 3 C 5 THR A 331 MET A 333 1 O MET A 333 N ILE A 226 SHEET 4 C 5 LEU A 234 PRO A 237 -1 N ARG A 235 O VAL A 332 SHEET 5 C 5 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 SHEET 1 D 5 GLN A 211 ASP A 212 0 SHEET 2 D 5 ILE A 203 ILE A 208 -1 N ILE A 208 O GLN A 211 SHEET 3 D 5 ILE A 283 MET A 288 -1 O TYR A 286 N ARG A 205 SHEET 4 D 5 GLN A 294 ILE A 300 -1 O PHE A 296 N LEU A 287 SHEET 5 D 5 ALA A 369 VAL A 375 -1 O GLU A 371 N ARG A 297 SHEET 1 E 3 VAL A 268 GLN A 271 0 SHEET 2 E 3 ASP A 317 PHE A 322 -1 O ASP A 318 N TRP A 270 SHEET 3 E 3 LEU A 306 VAL A 309 -1 N ARG A 307 O LYS A 321 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.10 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.11 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.06 CISPEP 1 SER A 22 PRO A 23 0 -3.90 CISPEP 2 SER A 22 PRO A 23 0 -6.10 CISPEP 3 ARG A 128 PRO A 129 0 1.30 CISPEP 4 TYR A 222 ASP A 223 0 2.52 CISPEP 5 GLY A 372 PRO A 373 0 -1.43 SITE 1 AC1 25 GLY A 11 GLN A 12 GLY A 13 LEU A 30 SITE 2 AC1 25 ASP A 32 GLY A 34 SER A 35 TYR A 71 SITE 3 AC1 25 THR A 72 GLN A 73 PHE A 108 TRP A 115 SITE 4 AC1 25 TYR A 198 ILE A 226 ASP A 228 SER A 229 SITE 5 AC1 25 GLY A 230 THR A 231 THR A 232 ASN A 233 SITE 6 AC1 25 ARG A 235 ARG A 307 SER A 325 ALA A 335 SITE 7 AC1 25 HOH A 640 SITE 1 AC2 4 SER A 22 PRO A 23 PRO A 91 ASN A 92 SITE 1 AC3 2 LEU A 377 HOH A 613 SITE 1 AC4 5 VAL A 93 THR A 94 URE A 407 HOH A 531 SITE 2 AC4 5 HOH A 672 SITE 1 AC5 1 URE A 402 SITE 1 AC6 2 GLY A 178 ILE A 179 SITE 1 AC7 1 GLY A 74 SITE 1 AC8 2 ARG A 61 THR A 82 SITE 1 AC9 3 ARG A 61 ASP A 62 CL A 397 SITE 1 BC1 8 ASP A 62 ARG A 64 LEU A 213 LYS A 214 SITE 2 BC1 8 MET A 215 HOH A 482 HOH A 529 HOH A 620 SITE 1 BC2 8 VAL A 67 TYR A 68 ARG A 128 PRO A 129 SITE 2 BC2 8 TRP A 189 HOH A 528 HOH A 654 HOH A 725 SITE 1 BC3 7 HIS A 45 PHE A 47 SER A 105 LYS A 107 SITE 2 BC3 7 PHE A 108 PHE A 109 HOH A 639 SITE 1 BC4 6 ASN A 28 HIS A 49 ARG A 50 GLU A 116 SITE 2 BC4 6 HOH A 513 HOH A 688 SITE 1 BC5 8 LEU A 84 THR A 94 ARG A 96 GLN A 143 SITE 2 BC5 8 CL A 396 HOH A 526 HOH A 531 HOH A 709 SITE 1 BC6 6 THR A 26 PRO A 88 HIS A 89 HOH A 455 SITE 2 BC6 6 HOH A 571 HOH A 674 SITE 1 BC7 6 PHE A -1 SER A 22 SER A 58 PRO A 147 SITE 2 BC7 6 GLY A 177 HOH A 524 SITE 1 BC8 6 ILE A 208 ASN A 209 GLN A 211 SER A 247 SITE 2 BC8 6 ALA A 250 ALA A 251 SITE 1 BC9 6 ASN A 209 ALA A 251 ASN A 278 ILE A 279 SITE 2 BC9 6 PHE A 280 ARG A 366 SITE 1 CC1 6 THR A 292 ASN A 293 ASP A 378 MET A 379 SITE 2 CC1 6 GLU A 380 HOH A 683 SITE 1 CC2 6 TYR A 51 GLN A 53 GLN A 55 LYS A 218 SITE 2 CC2 6 HOH A 685 HOH A 695 SITE 1 CC3 5 ARG A 235 SER A 328 HOH A 628 HOH A 696 SITE 2 CC3 5 HOH A 722 CRYST1 104.548 128.202 76.535 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009565 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013066 0.00000