PDB Short entry for 2VA7 HEADER HYDROLASE 30-AUG-07 2VA7 TITLE X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 27 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1 .; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEASE DOMAIN, RESIDUES 14-453; COMPND 5 SYNONYM: BETA-SITE APP CLEAVING ENZYME 1, BETA-SITE AMYLOID PRECURSOR COMPND 6 PROTEIN CLEAVING ENZYME 1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2, COMPND 7 MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2; 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 ORGAN: BRAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS BASE, ZYMOGEN, PROTEASE, MEMBRANE, HYDROLASE, ALZHEIMER'S DISEASE, KEYWDS 2 ALTERNATIVE SPLICING, MEMAPSIN 2, GLYCOPROTEIN, TRANSMEMBRANE, BETA- KEYWDS 3 SECRETASE, ASPARTYL PROTEASE, ASPARTIC PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.EDWARDS,J.S.ALBERT,M.SYLVESTER,D.AHARONY,D.ANDISIK,O.CALLAGHAN, AUTHOR 2 J.B.CAMPBELL,R.A.CARR,G.CHESSARI,M.CONGREVE,M.FREDERICKSON, AUTHOR 3 R.H.A.FOLMER,S.GESCHWINDNER,G.KOETHER,K.KOLMODIN,J.KRUMRINE, AUTHOR 4 R.C.MAUGER,C.W.MURRAY,L.L.OLSSON,S.PATEL,N.SPEAR,G.TIAN REVDAT 4 13-DEC-23 2VA7 1 REMARK REVDAT 3 24-FEB-09 2VA7 1 VERSN REVDAT 2 04-DEC-07 2VA7 1 JRNL REVDAT 1 13-NOV-07 2VA7 0 JRNL AUTH P.D.EDWARDS,J.S.ALBERT,M.SYLVESTER,D.AHARONY,D.ANDISIK, JRNL AUTH 2 O.CALLAGHAN,J.B.CAMPBELL,R.A.CARR,G.CHESSARI,M.CONGREVE, JRNL AUTH 3 M.FREDERICKSON,R.H.A.FOLMER,S.GESCHWINDNER,G.KOETHER, JRNL AUTH 4 K.KOLMODIN,J.KRUMRINE,R.C.MAUGER,C.W.MURRAY,L.L.OLSSON, JRNL AUTH 5 S.PATEL,N.SPEAR,G.TIAN JRNL TITL APPLICATION OF FRAGMENT-BASED LEAD GENERATION TO THE JRNL TITL 2 DISCOVERY OF NOVEL, CYCLIC AMIDINE BETA-SECRETASE INHIBITORS JRNL TITL 3 WITH NANOMOLAR POTENCY, CELLULAR ACTIVITY, AND HIGH LIGAND JRNL TITL 4 EFFICIENCY. JRNL REF J.MED.CHEM. V. 50 5912 2007 JRNL REFN ISSN 0022-2623 JRNL PMID 17985862 JRNL DOI 10.1021/JM070829P REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019G REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1378 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1881 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2948 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 203 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 0.37000 REMARK 3 B12 (A**2) : -0.12000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.245 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.219 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.667 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3054 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2044 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4155 ; 1.493 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4952 ; 0.902 ; 2.990 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 7.999 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;34.125 ;23.407 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 485 ;17.205 ;15.062 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.501 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 448 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3420 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 650 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 629 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2228 ; 0.208 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1464 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1586 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 55 ; 0.211 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 22 ; 0.222 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 61 ; 0.281 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.220 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1855 ; 0.069 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3001 ; 0.093 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1199 ; 0.094 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1154 ; 0.111 ; 7.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VA7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1290033637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.07000 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42000 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: C-SEARCH REMARK 200 STARTING MODEL: PDB ENTRY 1W50 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.11333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.22667 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 84.17000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 140.28333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.05667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.11333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 112.22667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 140.28333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 84.17000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 28.05667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.9 KCAL/MOL 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 350 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.05667 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 56 TO LYS REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 57 TO LYS 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 -62 REMARK 465 ALA A -61 REMARK 465 SER A -60 REMARK 465 MET A -59 REMARK 465 THR A -58 REMARK 465 GLY A -57 REMARK 465 GLY A -56 REMARK 465 GLN A -55 REMARK 465 GLN A -54 REMARK 465 MET A -53 REMARK 465 GLY A -52 REMARK 465 ARG A -51 REMARK 465 GLY A -50 REMARK 465 SER A -49 REMARK 465 MET A -48 REMARK 465 ALA A -47 REMARK 465 GLY A -46 REMARK 465 VAL A -45 REMARK 465 LEU A -44 REMARK 465 PRO A -43 REMARK 465 ALA A -42 REMARK 465 HIS A -41 REMARK 465 GLY A -40 REMARK 465 THR A -39 REMARK 465 GLN A -38 REMARK 465 HIS A -37 REMARK 465 GLY A -36 REMARK 465 ILE A -35 REMARK 465 ARG A -34 REMARK 465 LEU A -33 REMARK 465 PRO A -32 REMARK 465 LEU A -31 REMARK 465 ARG A -30 REMARK 465 SER A -29 REMARK 465 GLY A -28 REMARK 465 LEU A -27 REMARK 465 GLY A -26 REMARK 465 GLY A -25 REMARK 465 ALA A -24 REMARK 465 PRO A -23 REMARK 465 LEU A -22 REMARK 465 GLY A -21 REMARK 465 LEU A -20 REMARK 465 ARG 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 LYS A -5 REMARK 465 LYS A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 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 VAL A 170 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 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 ILE A 386 CA C O CB CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN A 55 O HOH A 1737 1.90 REMARK 500 OG SER A 22 OG1 THR A 59 2.08 REMARK 500 O HOH A 1568 O HOH A 1677 2.10 REMARK 500 O HOH A 1513 O HOH A 1589 2.10 REMARK 500 O HOH A 1648 O HOH A 1716 2.11 REMARK 500 O PRO A 281 OH TYR A 305 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 OH TYR A 222 OE1 GLU A 242 12555 2.18 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 HIS A 89 48.58 -101.82 REMARK 500 PHE A 108 -73.92 -102.84 REMARK 500 ALA A 122 -169.84 -76.19 REMARK 500 CYS A 155 -75.62 -101.26 REMARK 500 TRP A 197 -86.17 -136.28 REMARK 500 ASN A 209 -47.62 78.62 REMARK 500 SER A 252 54.35 -106.57 REMARK 500 THR A 254 -70.08 -48.12 REMARK 500 GLN A 316 53.60 -151.09 REMARK 500 ALA A 323 33.40 -88.17 REMARK 500 GLU A 364 36.28 -90.27 REMARK 500 PHE A 365 -90.09 -124.52 REMARK 500 ASP A 381 -5.33 -57.20 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 198 149.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1605 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A1715 DISTANCE = 7.48 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C27 A1505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M4H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED WITHINHIBITOR OM00-3 REMARK 900 RELATED ID: 1SGZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UNBOUND BETA-SECRETASE CATALYTICDOMAIN. REMARK 900 RELATED ID: 1W50 RELATED DB: PDB REMARK 900 APO STRUCTURE OF BACE (BETA SECRETASE) REMARK 900 RELATED ID: 1W51 RELATED DB: PDB REMARK 900 BACE (BETA SECRETASE) IN COMPLEX WITH A NANOMOLAR NON-PEPTIDIC REMARK 900 INHIBITOR REMARK 900 RELATED ID: 1XS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CYCLOAMIDE-URETHANE- DERIVED NOVELINHIBITOR REMARK 900 BOUND TO HUMAN BRAIN MEMAPSIN 2 (BETA-SECRETASE). REMARK 900 RELATED ID: 1YM4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AMK640 REMARK 900 RELATED ID: 1FKN RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-SECRETASE COMPLEXED WITH INHIBITOR REMARK 900 RELATED ID: 1PY1 RELATED DB: PDB REMARK 900 COMPLEX OF GGA1-VHS DOMAIN AND BETA- SECRETASE C- REMARK 900 TERMINALPHOSPHOPEPTIDE REMARK 900 RELATED ID: 1TQF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH L-124,671 REMARK 900 RELATED ID: 1UJJ RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C -TERMINAL PEPTIDEFROM BACE REMARK 900 RELATED ID: 1UJK RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C -TERMINALPHOSPHOPEPTIDE REMARK 900 FROM BACE REMARK 900 RELATED ID: 1XN2 RELATED DB: PDB REMARK 900 NEW SUBSTRATE BINDING POCKETS FOR BETA- SECRETASE. REMARK 900 RELATED ID: 1XN3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE BOUND TO A LONGINHIBITOR WITH REMARK 900 ADDITIONAL UPSTREAM RESIDUES. REMARK 900 RELATED ID: 1YM2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AUR200 REMARK 900 RELATED ID: 2B8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH L-000384950 REMARK 900 RELATED ID: 2B8V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA-SECRETASE COMPLEXED WITH L-L000430, REMARK 900 469 REMARK 900 RELATED ID: 2VA5 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 8C REMARK 900 RELATED ID: 2VA6 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 24 DBREF 2VA7 A -62 -48 PDB 2VA7 2VA7 -62 -48 DBREF 2VA7 A -47 392 UNP P56817 BACE1_HUMAN 14 453 SEQADV 2VA7 LYS A -5 UNP P56817 ARG 56 ENGINEERED MUTATION SEQADV 2VA7 LYS A -4 UNP P56817 ARG 57 ENGINEERED MUTATION SEQRES 1 A 455 MET ALA SER MET THR GLY GLY GLN GLN MET GLY ARG GLY SEQRES 2 A 455 SER MET ALA GLY VAL LEU PRO ALA HIS GLY THR GLN HIS SEQRES 3 A 455 GLY ILE ARG LEU PRO LEU ARG SER GLY LEU GLY GLY ALA SEQRES 4 A 455 PRO LEU GLY LEU ARG LEU PRO ARG GLU THR ASP GLU GLU SEQRES 5 A 455 PRO GLU GLU PRO GLY LYS LYS GLY SER PHE VAL GLU MET SEQRES 6 A 455 VAL ASP ASN LEU ARG GLY LYS SER GLY GLN GLY TYR TYR SEQRES 7 A 455 VAL GLU MET THR VAL GLY SER PRO PRO GLN THR LEU ASN SEQRES 8 A 455 ILE LEU VAL ASP THR GLY SER SER ASN PHE ALA VAL GLY SEQRES 9 A 455 ALA ALA PRO HIS PRO PHE LEU HIS ARG TYR TYR GLN ARG SEQRES 10 A 455 GLN LEU SER SER THR TYR ARG ASP LEU ARG LYS GLY VAL SEQRES 11 A 455 TYR VAL PRO TYR THR GLN GLY LYS TRP GLU GLY GLU LEU SEQRES 12 A 455 GLY THR ASP LEU VAL SER ILE PRO HIS GLY PRO ASN VAL SEQRES 13 A 455 THR VAL ARG ALA ASN ILE ALA ALA ILE THR GLU SER ASP SEQRES 14 A 455 LYS PHE PHE ILE ASN GLY SER ASN TRP GLU GLY ILE LEU SEQRES 15 A 455 GLY LEU ALA TYR ALA GLU ILE ALA ARG PRO ASP ASP SER SEQRES 16 A 455 LEU GLU PRO PHE PHE ASP SER LEU VAL LYS GLN THR HIS SEQRES 17 A 455 VAL PRO ASN LEU PHE SER LEU GLN LEU CYS GLY ALA GLY SEQRES 18 A 455 PHE PRO LEU ASN GLN SER GLU VAL LEU ALA SER VAL GLY SEQRES 19 A 455 GLY SER MET ILE ILE GLY GLY ILE ASP HIS SER LEU TYR SEQRES 20 A 455 THR GLY SER LEU TRP TYR THR PRO ILE ARG ARG GLU TRP SEQRES 21 A 455 TYR TYR GLU VAL ILE ILE VAL ARG VAL GLU ILE ASN GLY SEQRES 22 A 455 GLN ASP LEU LYS MET ASP CYS LYS GLU TYR ASN TYR ASP SEQRES 23 A 455 LYS SER ILE VAL ASP SER GLY THR THR ASN LEU ARG LEU SEQRES 24 A 455 PRO LYS LYS VAL PHE GLU ALA ALA VAL LYS SER ILE LYS SEQRES 25 A 455 ALA ALA SER SER THR GLU LYS PHE PRO ASP GLY PHE TRP SEQRES 26 A 455 LEU GLY GLU GLN LEU VAL CYS TRP GLN ALA GLY THR THR SEQRES 27 A 455 PRO TRP ASN ILE PHE PRO VAL ILE SER LEU TYR LEU MET SEQRES 28 A 455 GLY GLU VAL THR ASN GLN SER PHE ARG ILE THR ILE LEU SEQRES 29 A 455 PRO GLN GLN TYR LEU ARG PRO VAL GLU ASP VAL ALA THR SEQRES 30 A 455 SER GLN ASP ASP CYS TYR LYS PHE ALA ILE SER GLN SER SEQRES 31 A 455 SER THR GLY THR VAL MET GLY ALA VAL ILE MET GLU GLY SEQRES 32 A 455 PHE TYR VAL VAL PHE ASP ARG ALA ARG LYS ARG ILE GLY SEQRES 33 A 455 PHE ALA VAL SER ALA CYS HIS VAL HIS ASP GLU PHE ARG SEQRES 34 A 455 THR ALA ALA VAL GLU GLY PRO PHE VAL THR LEU ASP MET SEQRES 35 A 455 GLU ASP CYS GLY TYR ASN ILE PRO GLN THR ASP GLU SER HET IOD A1502 1 HET IOD A1503 1 HET IOD A1504 1 HET C27 A1505 26 HETNAM IOD IODIDE ION HETNAM C27 (6R)-2-AMINO-6-[2-(3'-METHOXYBIPHENYL-3-YL)ETHYL]-3,6- HETNAM 2 C27 DIMETHYL-5,6-DIHYDROPYRIMIDIN-4(3H)-ONE FORMUL 2 IOD 3(I 1-) FORMUL 5 C27 C21 H25 N3 O2 FORMUL 6 HOH *203(H2 O) HELIX 1 1 GLN A 53 SER A 57 5 5 HELIX 2 2 TYR A 123 ALA A 127 5 5 HELIX 3 3 PRO A 135 THR A 144 1 10 HELIX 4 4 ASP A 180 SER A 182 5 3 HELIX 5 5 ASP A 216 TYR A 222 5 7 HELIX 6 6 LYS A 238 SER A 252 1 15 HELIX 7 7 PRO A 258 LEU A 263 1 6 HELIX 8 8 PRO A 276 PHE A 280 5 5 HELIX 9 9 LEU A 301 TYR A 305 1 5 HELIX 10 10 GLY A 334 GLU A 339 1 6 HELIX 11 11 ARG A 347 ARG A 349 5 3 HELIX 12 12 MET A 379 GLY A 383 5 5 SHEET 1 AA 7 LEU A 6 LYS A 9 0 SHEET 2 AA 7 GLY A 13 VAL A 20 -1 O GLY A 13 N LYS A 9 SHEET 3 AA 7 GLN A 25 ASP A 32 -1 O GLN A 25 N VAL A 20 SHEET 4 AA 7 GLY A 117 GLY A 120 1 O GLY A 117 N LEU A 30 SHEET 5 AA 7 PHE A 38 GLY A 41 -1 O ALA A 39 N ILE A 118 SHEET 6 AA 7 VAL A 95 ASP A 106 1 O ALA A 100 N VAL A 40 SHEET 7 AA 7 GLY A 74 SER A 86 -1 O LYS A 75 N ASP A 106 SHEET 1 AB 3 LEU A 6 LYS A 9 0 SHEET 2 AB 3 GLY A 13 VAL A 20 -1 O GLY A 13 N LYS A 9 SHEET 3 AB 3 GLY A 74 SER A 86 -1 O SER A 86 N THR A 19 SHEET 1 AC 5 GLY A 172 ILE A 176 0 SHEET 2 AC 5 PHE A 150 LEU A 154 -1 O SER A 151 N ILE A 175 SHEET 3 AC 5 PHE A 341 ASP A 346 -1 O VAL A 343 N LEU A 152 SHEET 4 AC 5 ARG A 351 SER A 357 -1 O ARG A 351 N ASP A 346 SHEET 5 AC 5 TYR A 184 PRO A 192 -1 O THR A 185 N VAL A 356 SHEET 1 AD 5 GLN A 211 ASP A 212 0 SHEET 2 AD 5 ILE A 203 ILE A 208 -1 N ILE A 208 O GLN A 211 SHEET 3 AD 5 ILE A 283 MET A 288 -1 O SER A 284 N GLU A 207 SHEET 4 AD 5 GLN A 294 ILE A 300 -1 O PHE A 296 N LEU A 287 SHEET 5 AD 5 ALA A 369 VAL A 375 -1 O ALA A 369 N THR A 299 SHEET 1 AE 2 SER A 225 VAL A 227 0 SHEET 2 AE 2 THR A 331 MET A 333 1 O THR A 331 N ILE A 226 SHEET 1 AF 2 LEU A 234 PRO A 237 0 SHEET 2 AF 2 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 SHEET 1 AG 3 VAL A 268 TRP A 270 0 SHEET 2 AG 3 ASP A 318 PHE A 322 -1 O ASP A 318 N TRP A 270 SHEET 3 AG 3 LEU A 306 PRO A 308 -1 O ARG A 307 N LYS A 321 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.08 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.06 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.03 CISPEP 1 SER A 22 PRO A 23 0 0.98 CISPEP 2 ARG A 128 PRO A 129 0 5.63 CISPEP 3 TYR A 222 ASP A 223 0 -11.49 CISPEP 4 GLY A 372 PRO A 373 0 -3.73 SITE 1 AC1 3 GLU A 104 SER A 105 HOH A1575 SITE 1 AC2 4 PHE A 47 ASP A 106 LYS A 107 HOH A1649 SITE 1 AC3 2 GLN A 55 ARG A 349 SITE 1 AC4 14 SER A 10 GLY A 11 GLN A 12 GLY A 13 SITE 2 AC4 14 ASP A 32 GLY A 34 TYR A 71 PHE A 108 SITE 3 AC4 14 TRP A 115 ASP A 228 SER A 229 GLY A 230 SITE 4 AC4 14 THR A 231 THR A 232 CRYST1 102.687 102.687 168.340 90.00 90.00 120.00 P 61 2 2 12 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 0.009738 0.005622 0.000000 0.00000 SCALE2 0.000000 0.011245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005940 0.00000