PDB Short entry for 4J1C HEADER HYDROLASE/HYDROLASE INHIBITOR 01-FEB-13 4J1C TITLE CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-CYANO-PYRIDINE-2- TITLE 2 CARBOXYLIC ACID [3-((S)-2-AMINO-5,5-DIFLUORO-4-FLUOROMETHYL-5,6- TITLE 3 DIHYDRO-4H-[1,3]OXAZIN-4-YL)-4-FLUORO-PHENYL]-AMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID COMPND 5 PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, COMPND 6 MEMAPSIN-2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; COMPND 7 EC: 3.4.23.46; COMPND 8 ENGINEERED: YES; COMPND 9 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: BACE1, BACE, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.KUGLSTATTER,M.STIHLE REVDAT 3 15-NOV-17 4J1C 1 REMARK REVDAT 2 19-JUN-13 4J1C 1 JRNL REVDAT 1 01-MAY-13 4J1C 0 JRNL AUTH H.HILPERT,W.GUBA,T.J.WOLTERING,W.WOSTL,E.PINARD,H.MAUSER, JRNL AUTH 2 A.V.MAYWEG,M.ROGERS-EVANS,R.HUMM,D.KRUMMENACHER,T.MUSER, JRNL AUTH 3 C.SCHNIDER,H.JACOBSEN,L.OZMEN,A.BERGADANO,D.W.BANNER, JRNL AUTH 4 R.HOCHSTRASSER,A.KUGLSTATTER,P.DAVID-PIERSON,H.FISCHER, JRNL AUTH 5 A.POLARA,R.NARQUIZIAN JRNL TITL BETA-SECRETASE (BACE1) INHIBITORS WITH HIGH IN VIVO EFFICACY JRNL TITL 2 SUITABLE FOR CLINICAL EVALUATION IN ALZHEIMER S DISEASE JRNL REF J.MED.CHEM. V. 56 3980 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23590342 JRNL DOI 10.1021/JM400225M REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 33889 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1787 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2453 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2918 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : 0.08000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.280 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3061 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4170 ; 2.022 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 7.174 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;32.332 ;23.478 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 486 ;15.033 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;14.113 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2352 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 601 A 853 REMARK 3 RESIDUE RANGE : A 501 A 504 REMARK 3 RESIDUE RANGE : A 57 A 446 REMARK 3 ORIGIN FOR THE GROUP (A): -13.3673 -40.9675 0.0844 REMARK 3 T TENSOR REMARK 3 T11: 0.0048 T22: 0.0230 REMARK 3 T33: 0.0926 T12: -0.0095 REMARK 3 T13: -0.0106 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 2.0442 L22: 0.9090 REMARK 3 L33: 1.1243 L12: -1.0703 REMARK 3 L13: 0.8322 L23: -0.2947 REMARK 3 S TENSOR REMARK 3 S11: 0.0022 S12: -0.0308 S13: -0.1187 REMARK 3 S21: -0.0012 S22: 0.0133 S23: 0.0849 REMARK 3 S31: 0.0016 S32: -0.0168 S33: -0.0155 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: NULL REMARK 4 REMARK 4 4J1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-12 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35745 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 49.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5M SODIUM FORMATE, 100MM HEPES, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 56.49600 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 112.99200 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 84.74400 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 141.24000 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 28.24800 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 56.49600 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 112.99200 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 141.24000 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 84.74400 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 28.24800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 783 LIES ON A SPECIAL POSITION. 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 GLU A 46 REMARK 465 THR A 47 REMARK 465 ASP A 48 REMARK 465 GLU A 49 REMARK 465 GLU A 50 REMARK 465 PRO A 51 REMARK 465 GLU A 52 REMARK 465 GLU A 53 REMARK 465 PRO A 54 REMARK 465 GLY A 55 REMARK 465 ARG A 56 REMARK 465 GLY A 219 REMARK 465 PHE A 220 REMARK 465 PRO A 221 REMARK 465 LEU A 222 REMARK 465 ASN A 223 REMARK 465 GLN A 224 REMARK 465 SER A 225 REMARK 465 GLU A 226 REMARK 465 VAL A 227 REMARK 465 LEU A 228 REMARK 465 ALA A 229 REMARK 465 GLU A 371 REMARK 465 ASP A 372 REMARK 465 VAL A 373 REMARK 465 ALA A 374 REMARK 465 THR A 375 REMARK 465 SER A 376 REMARK 465 GLN A 377 REMARK 465 ASP A 378 REMARK 465 ILE A 447 REMARK 465 PRO A 448 REMARK 465 GLN A 449 REMARK 465 THR A 450 REMARK 465 ASP A 451 REMARK 465 GLU A 452 REMARK 465 SER A 453 REMARK 465 THR A 454 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 OE2 GLU A 303 O HOH A 788 1.43 REMARK 500 O HOH A 674 O HOH A 771 1.63 REMARK 500 O HOH A 668 O HOH A 746 1.99 REMARK 500 NZ LYS A 136 OE1 GLU A 165 2.03 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 O HOH A 794 O HOH A 794 10444 1.61 REMARK 500 O HOH A 839 O HOH A 839 10444 1.87 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 SER A 308 CB SER A 308 OG -0.079 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 189 NE - CZ - NH1 ANGL. DEV. = 4.0 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 60 54.10 -146.14 REMARK 500 GLU A 177 18.09 -140.39 REMARK 500 TRP A 258 -85.46 -140.22 REMARK 500 SER A 314 1.33 -60.83 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 258 TYR A 259 149.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 793 O REMARK 620 2 THR A 205 O 78.3 REMARK 620 3 HOH A 733 O 165.1 101.0 REMARK 620 4 VAL A 202 O 93.7 84.7 101.1 REMARK 620 5 HOH A 767 O 85.6 158.8 98.1 82.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 672 O REMARK 620 2 TYR A 245 O 98.7 REMARK 620 3 HIS A 242 O 155.3 82.0 REMARK 620 4 HOH A 801 O 106.0 70.3 97.5 REMARK 620 5 HOH A 745 O 58.1 139.9 106.1 143.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1HO A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J0P RELATED DB: PDB REMARK 900 RELATED ID: 4J0T RELATED DB: PDB REMARK 900 RELATED ID: 4J0V RELATED DB: PDB REMARK 900 RELATED ID: 4J0Y RELATED DB: PDB REMARK 900 RELATED ID: 4J0Z RELATED DB: PDB REMARK 900 RELATED ID: 4J17 RELATED DB: PDB REMARK 900 RELATED ID: 4J1E RELATED DB: PDB REMARK 900 RELATED ID: 4J1F RELATED DB: PDB REMARK 900 RELATED ID: 4J1H RELATED DB: PDB REMARK 900 RELATED ID: 4J1I RELATED DB: PDB REMARK 900 RELATED ID: 4J1K RELATED DB: PDB DBREF 4J1C A 46 454 UNP P56817 BACE1_HUMAN 46 454 SEQADV 4J1C ALA A 307 UNP P56817 LYS 307 ENGINEERED MUTATION SEQRES 1 A 409 GLU THR ASP GLU GLU PRO GLU GLU PRO GLY ARG ARG GLY SEQRES 2 A 409 SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER SEQRES 3 A 409 GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO SEQRES 4 A 409 PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SER SEQRES 5 A 409 ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS SEQRES 6 A 409 ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP SEQRES 7 A 409 LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS SEQRES 8 A 409 TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO SEQRES 9 A 409 HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA SEQRES 10 A 409 ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN SEQRES 11 A 409 TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA SEQRES 12 A 409 ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU SEQRES 13 A 409 VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN SEQRES 14 A 409 LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL SEQRES 15 A 409 LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE SEQRES 16 A 409 ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR PRO SEQRES 17 A 409 ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG SEQRES 18 A 409 VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS SEQRES 19 A 409 GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR SEQRES 20 A 409 THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA SEQRES 21 A 409 VAL ALA SER ILE LYS ALA ALA SER SER THR GLU LYS PHE SEQRES 22 A 409 PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP SEQRES 23 A 409 GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SEQRES 24 A 409 SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE SEQRES 25 A 409 ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL SEQRES 26 A 409 GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE SEQRES 27 A 409 ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY ALA SEQRES 28 A 409 VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA SEQRES 29 A 409 ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL SEQRES 30 A 409 HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE SEQRES 31 A 409 VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO SEQRES 32 A 409 GLN THR ASP GLU SER THR HET NA A 501 1 HET NA A 502 1 HET DMS A 503 4 HET 1HO A 504 29 HETNAM NA SODIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM 1HO N-{3-[(4S)-2-AMINO-5,5-DIFLUORO-4-(FLUOROMETHYL)-5,6- HETNAM 2 1HO DIHYDRO-4H-1,3-OXAZIN-4-YL]-4-FLUOROPHENYL}-5- HETNAM 3 1HO CYANOPYRIDINE-2-CARBOXAMIDE FORMUL 2 NA 2(NA 1+) FORMUL 4 DMS C2 H6 O S FORMUL 5 1HO C18 H13 F4 N5 O2 FORMUL 6 HOH *253(H2 O) HELIX 1 1 PHE A 60 VAL A 64 5 5 HELIX 2 2 GLN A 114 SER A 118 5 5 HELIX 3 3 TYR A 184 ALA A 188 5 5 HELIX 4 4 PRO A 196 THR A 205 1 10 HELIX 5 5 ASP A 241 SER A 243 5 3 HELIX 6 6 ASP A 277 TYR A 283 5 7 HELIX 7 7 LYS A 299 SER A 313 1 15 HELIX 8 8 PRO A 319 LEU A 324 1 6 HELIX 9 9 PRO A 337 PHE A 341 5 5 HELIX 10 10 LEU A 362 TYR A 366 1 5 HELIX 11 11 GLY A 395 GLU A 400 1 6 HELIX 12 12 ARG A 408 ARG A 410 5 3 HELIX 13 13 MET A 440 GLY A 444 5 5 SHEET 1 A 9 ARG A 122 PRO A 131 0 SHEET 2 A 9 LYS A 136 SER A 147 -1 O TRP A 137 N VAL A 130 SHEET 3 A 9 TYR A 75 VAL A 81 -1 N THR A 80 O SER A 147 SHEET 4 A 9 LEU A 67 GLY A 69 -1 N ARG A 68 O TYR A 76 SHEET 5 A 9 VAL A 231 ILE A 237 -1 O GLY A 233 N LEU A 67 SHEET 6 A 9 PHE A 211 CYS A 216 -1 N GLN A 214 O SER A 234 SHEET 7 A 9 PHE A 402 ASP A 407 -1 O PHE A 406 N PHE A 211 SHEET 8 A 9 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403 SHEET 9 A 9 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413 SHEET 1 B13 ARG A 122 PRO A 131 0 SHEET 2 B13 LYS A 136 SER A 147 -1 O TRP A 137 N VAL A 130 SHEET 3 B13 VAL A 156 ASP A 167 -1 O ALA A 162 N GLU A 140 SHEET 4 B13 PHE A 99 GLY A 102 1 N VAL A 101 O ILE A 163 SHEET 5 B13 GLY A 178 GLY A 181 -1 O ILE A 179 N ALA A 100 SHEET 6 B13 GLN A 86 ASP A 93 1 N LEU A 91 O LEU A 180 SHEET 7 B13 TYR A 75 VAL A 81 -1 N MET A 79 O LEU A 88 SHEET 8 B13 LEU A 67 GLY A 69 -1 N ARG A 68 O TYR A 76 SHEET 9 B13 VAL A 231 ILE A 237 -1 O GLY A 233 N LEU A 67 SHEET 10 B13 PHE A 211 CYS A 216 -1 N GLN A 214 O SER A 234 SHEET 11 B13 PHE A 402 ASP A 407 -1 O PHE A 406 N PHE A 211 SHEET 12 B13 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403 SHEET 13 B13 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413 SHEET 1 C 5 GLU A 261 VAL A 262 0 SHEET 2 C 5 SER A 286 VAL A 288 -1 O SER A 286 N VAL A 262 SHEET 3 C 5 THR A 392 MET A 394 1 O MET A 394 N ILE A 287 SHEET 4 C 5 LEU A 295 PRO A 298 -1 N ARG A 296 O VAL A 393 SHEET 5 C 5 ILE A 385 SER A 388 1 O SER A 386 N LEU A 297 SHEET 1 D 5 GLN A 272 ASP A 273 0 SHEET 2 D 5 ILE A 264 ILE A 269 -1 N ILE A 269 O GLN A 272 SHEET 3 D 5 ILE A 344 MET A 349 -1 O TYR A 347 N ARG A 266 SHEET 4 D 5 GLN A 355 ILE A 361 -1 O ILE A 359 N LEU A 346 SHEET 5 D 5 ALA A 430 VAL A 436 -1 O GLU A 432 N ARG A 358 SHEET 1 E 3 VAL A 329 CYS A 330 0 SHEET 2 E 3 CYS A 380 PHE A 383 -1 O TYR A 381 N VAL A 329 SHEET 3 E 3 LEU A 367 PRO A 369 -1 N ARG A 368 O LYS A 382 SSBOND 1 CYS A 216 CYS A 420 1555 1555 2.14 SSBOND 2 CYS A 278 CYS A 443 1555 1555 2.10 SSBOND 3 CYS A 330 CYS A 380 1555 1555 2.10 LINK NA NA A 502 O HOH A 793 1555 1555 2.22 LINK O THR A 205 NA NA A 502 1555 1555 2.25 LINK NA NA A 502 O HOH A 733 1555 1555 2.27 LINK O VAL A 202 NA NA A 502 1555 1555 2.38 LINK NA NA A 501 O HOH A 672 1555 1555 2.45 LINK O TYR A 245 NA NA A 501 1555 1555 2.47 LINK O HIS A 242 NA NA A 501 1555 1555 2.47 LINK NA NA A 501 O HOH A 801 1555 1555 2.51 LINK NA NA A 502 O HOH A 767 1555 1555 2.73 LINK NA NA A 501 O HOH A 745 1555 1555 3.10 CISPEP 1 SER A 83 PRO A 84 0 -4.01 CISPEP 2 ARG A 189 PRO A 190 0 7.00 CISPEP 3 TYR A 283 ASP A 284 0 2.23 CISPEP 4 GLY A 433 PRO A 434 0 -3.73 SITE 1 AC1 5 HIS A 242 TYR A 245 HOH A 672 HOH A 745 SITE 2 AC1 5 HOH A 801 SITE 1 AC2 5 VAL A 202 THR A 205 HOH A 733 HOH A 767 SITE 2 AC2 5 HOH A 793 SITE 1 AC3 3 ARG A 157 ASN A 159 GLU A 195 SITE 1 AC4 16 GLY A 72 GLN A 73 GLY A 74 LEU A 91 SITE 2 AC4 16 ASP A 93 SER A 96 TYR A 132 PHE A 169 SITE 3 AC4 16 ILE A 171 ILE A 179 ASP A 289 SER A 290 SITE 4 AC4 16 GLY A 291 THR A 293 ALA A 396 HOH A 846 CRYST1 102.452 102.452 169.488 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 0.009761 0.005635 0.000000 0.00000 SCALE2 0.000000 0.011271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005900 0.00000