PDB Short entry for 3UFL HEADER HYDROLASE/HYDROLASE INHIBITOR 01-NOV-11 3UFL TITLE DISCOVERY OF PYRROLIDINE-BASED B-SECRETASE INHIBITORS: LEAD TITLE 2 ADVANCEMENT THROUGH CONFORMATIONAL DESIGN FOR MAINTENANCE OF LIGAND TITLE 3 BINDING EFFICIENCY COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 58-446; COMPND 5 SYNONYM: BACE1, 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BACE1, BACE, KIAA1149 KEYWDS ASPARTYL PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.ALLISON,S.MUNSHI,S.M.SOISSON REVDAT 1 18-JAN-12 3UFL 0 JRNL AUTH S.J.STACHEL,T.G.STEELE,A.PETROCCHI,S.J.HAUGABOOK, JRNL AUTH 2 G.MCGAUGHEY,M.KATHARINE HOLLOWAY,T.ALLISON,S.MUNSHI,P.ZUCK, JRNL AUTH 3 D.COLUSSI,K.TUGASHEVA,A.WOLFE,S.L.GRAHAM,J.P.VACCA JRNL TITL DISCOVERY OF PYRROLIDINE-BASED BETA-SECRETASE INHIBITORS: JRNL TITL 2 LEAD ADVANCEMENT THROUGH CONFORMATIONAL DESIGN FOR JRNL TITL 3 MAINTENANCE OF LIGAND BINDING EFFICIENCY. JRNL REF BIOORG.MED.CHEM.LETT. V. 22 240 2012 JRNL REFN ISSN 0960-894X JRNL PMID 22130130 JRNL DOI 10.1016/J.BMCL.2011.11.024 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 39826 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2038 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2520 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.3690 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2927 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 308 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -0.21000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.501 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3074 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4183 ; 1.158 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 6.280 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;32.672 ;23.723 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 475 ;12.860 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.676 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 449 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2344 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1379 ; 0.186 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2035 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 258 ; 0.123 ; 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): 75 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 35 ; 0.152 ; 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): 1904 ; 0.617 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3002 ; 1.097 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1344 ; 1.158 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1180 ; 1.979 ; 4.500 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 : 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 3UFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-11. REMARK 100 THE RCSB ID CODE IS RCSB068692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39870 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 273K 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 38.42300 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 38.42300 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 51.83400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.82100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.83400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.82100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.42300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.83400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.82100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.42300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.83400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.82100 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 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 GLU A 310 REMARK 465 ASP A 311 REMARK 465 VAL A 312 REMARK 465 ALA A 313 REMARK 465 THR A 314 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 LYS A 75 CG CD CE NZ REMARK 470 GLU A 77 CG 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 THR A 72 CZ ARG A 349 6554 2.06 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 GLN A 73 54.22 111.59 REMARK 500 LYS A 75 166.45 178.89 REMARK 500 PHE A 108 -61.40 -93.91 REMARK 500 ASN A 114 -0.93 72.50 REMARK 500 TRP A 197 -85.05 -137.23 REMARK 500 ALA A 272 116.66 -32.65 REMARK 500 ASP A 363 -166.49 -104.41 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 THR A 72 GLN A 73 -33.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 72 23.8 L L OUTSIDE RANGE REMARK 500 GLN A 73 20.9 L L OUTSIDE RANGE 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 508 A 449 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 453 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 454 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 455 DBREF 3UFL A 445 385 UNP P56817 BACE1_HUMAN 58 446 SEQRES 1 A 389 GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SEQRES 2 A 389 SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER SEQRES 3 A 389 PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SEQRES 4 A 389 SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU SEQRES 5 A 389 HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG SEQRES 6 A 389 ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY SEQRES 7 A 389 LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE SEQRES 8 A 389 PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA SEQRES 9 A 389 ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER SEQRES 10 A 389 ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE SEQRES 11 A 389 ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER SEQRES 12 A 389 LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU SEQRES 13 A 389 GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU SEQRES 14 A 389 VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY SEQRES 15 A 389 ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR SEQRES 16 A 389 PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL SEQRES 17 A 389 ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS SEQRES 18 A 389 LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY SEQRES 19 A 389 THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA SEQRES 20 A 389 ALA VAL LYS SER ILE LYS ALA ALA SER SER THR GLU LYS SEQRES 21 A 389 PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS SEQRES 22 A 389 TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL SEQRES 23 A 389 ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER SEQRES 24 A 389 PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO SEQRES 25 A 389 VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS SEQRES 26 A 389 PHE ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY SEQRES 27 A 389 ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG SEQRES 28 A 389 ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS SEQRES 29 A 389 VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO SEQRES 30 A 389 PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN HET 508 A 449 34 HET SO4 A 450 5 HET SO4 A 451 5 HET SO4 A 452 5 HET SO4 A 453 5 HET GOL A 454 6 HET GOL A 455 6 HETNAM 508 (1R,4'S)-3,4-DIHYDRO-2H-SPIRO[NAPHTHALENE-1,3'- HETNAM 2 508 PYRROLIDIN]-4'-YL[(2S,4R)-2,4-DIPHENYLPIPERIDIN-1- HETNAM 3 508 YL]METHANONE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 508 C31 H34 N2 O FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 HOH *308(H2 O) HELIX 1 1 PHE A 447 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 ARG A 347 ARG A 349 5 3 HELIX 13 13 ASP A 378 GLY A 383 5 6 SHEET 1 A 9 ARG A 61 PRO A 70 0 SHEET 2 A 9 LYS A 75 SER A 86 -1 O LEU A 80 N LYS A 65 SHEET 3 A 9 GLY A 13 VAL A 20 -1 N THR A 19 O SER A 86 SHEET 4 A 9 LEU A 6 LYS A 9 -1 N ARG A 7 O TYR A 15 SHEET 5 A 9 VAL A 170 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 LYS 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 ASP A 106 N LYS A 75 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 GLY A 13 VAL A 20 -1 N VAL A 20 O GLN A 25 SHEET 8 B13 LEU A 6 LYS A 9 -1 N ARG A 7 O TYR A 15 SHEET 9 B13 VAL A 170 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 ILE A 300 N ILE A 283 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 PRO A 308 -1 N ARG A 307 O LYS A 321 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.04 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.04 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.04 CISPEP 1 SER A 22 PRO A 23 0 -2.31 CISPEP 2 ARG A 128 PRO A 129 0 0.54 CISPEP 3 TYR A 222 ASP A 223 0 1.40 CISPEP 4 GLY A 372 PRO A 373 0 -3.49 SITE 1 AC1 16 LEU A 30 ASP A 32 GLY A 34 VAL A 69 SITE 2 AC1 16 PRO A 70 TYR A 71 GLN A 73 GLY A 74 SITE 3 AC1 16 LYS A 75 ASP A 106 LYS A 107 ILE A 126 SITE 4 AC1 16 ASP A 228 GLY A 230 THR A 231 GOL A 455 SITE 1 AC2 5 ARG A 235 GLN A 326 SER A 327 SER A 328 SITE 2 AC2 5 THR A 329 SITE 1 AC3 8 ARG A 96 ALA A 97 ASN A 98 GLU A 134 SITE 2 AC3 8 SER A 139 GLN A 143 HOH A 478 HOH A 739 SITE 1 AC4 3 ARG A 205 HOH A 535 HOH A 688 SITE 1 AC5 4 TYR A 51 GLN A 53 GLN A 55 LYS A 218 SITE 1 AC6 9 TYR A 68 PRO A 70 ARG A 128 SER A 187 SITE 2 AC6 9 LEU A 188 TRP A 189 HOH A 488 HOH A 494 SITE 3 AC6 9 HOH A 740 SITE 1 AC7 3 GLN A 12 GLY A 230 508 A 449 CRYST1 103.668 127.642 76.846 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 0.009646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013013 0.00000