HEADER HYDROLASE/HYDROLASE INHIBITOR 16-NOV-12 4I0J TITLE SPR AND STRUCTURAL ANALYSIS YIELD INSIGHT TOWARDS MECHANISM OF TITLE 2 INHIBITION OF BACE INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 57-453; 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 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 BACE ASP PROTEASE, HYDROLYSIS,, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.YAO,E.BRECHT REVDAT 1 06-MAR-13 4I0J 0 JRNL AUTH K.MONDAL,K.REGNSTROM,W.MORISHIGE,R.BARBOUR,P.BEROZA,N.YAO, JRNL AUTH 2 M.P.BOVA JRNL TITL SPR AND STRUCTURAL ANALYSIS YIELD INSIGHT TOWARDS MECHANISM JRNL TITL 2 OF INHIBITION OF BACE INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 24728 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1305 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) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1690 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3560 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3063 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23000 REMARK 3 B22 (A**2) : -1.93000 REMARK 3 B33 (A**2) : 3.15000 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): 0.250 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.920 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3184 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4328 ; 1.859 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 385 ; 7.751 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;34.772 ;23.673 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;17.063 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.369 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 465 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2448 ; 0.010 ; 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): 1923 ; 1.057 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3110 ; 1.845 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1261 ; 2.869 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1218 ; 4.363 ; 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 : 1.40 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 4I0J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-12. REMARK 100 THE RCSB ID CODE IS RCSB076151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : STRUCTURESTUDIO REMARK 200 DATA SCALING SOFTWARE : STRUCTURESTUDIO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39466 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 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 (%): 42.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BACE WAS CONCENTRATED TO 10MG/ML IN REMARK 280 100 MM BORATE PH 8.5. APO CRYSTALS WERE GROWN AT 277K IN 1 UL REMARK 280 WITH A 1:1(V/V) RATIO OF PROTEIN TO RESERVOIR, A SOLUTION OF 9% REMARK 280 PEG 8000, 100MM SODIUM ACETATE AND 10MM ZNCL2 , VAPOR DIFFUSION, REMARK 280 SITTING DROP 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 49.53150 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 49.53150 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 37.61400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.01950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.61400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.01950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.53150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.61400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.01950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.53150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.61400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.01950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -246.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 56 REMARK 465 ARG A 57 REMARK 465 ALA A 218 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 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 HIS A 461 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 O HOH A 649 O HOH A 820 1.86 REMARK 500 O HOH A 602 O HOH A 720 2.03 REMARK 500 O HOH A 784 O HOH A 810 2.04 REMARK 500 O HOH A 701 O HOH A 739 2.05 REMARK 500 O HOH A 754 O HOH A 796 2.10 REMARK 500 O HOH A 661 O HOH A 735 2.16 REMARK 500 ND2 ASN A 98 O HOH A 661 2.16 REMARK 500 O ASP A 439 O HOH A 720 2.19 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 PRO A 107 C - N - CA ANGL. DEV. = 10.9 DEGREES REMARK 500 ASP A 284 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 LEU A 438 CA - CB - CG ANGL. DEV. = 16.3 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 ASP A 65 30.63 71.45 REMARK 500 TYR A 132 -147.76 -117.96 REMARK 500 GLN A 134 -42.38 -130.98 REMARK 500 HIS A 150 50.55 -101.86 REMARK 500 TRP A 258 -84.77 -138.03 REMARK 500 SER A 314 -6.98 -57.52 REMARK 500 ALA A 333 123.49 -21.59 REMARK 500 ASN A 354 -8.56 73.67 REMARK 500 THR A 437 -124.11 -147.28 REMARK 500 LEU A 438 114.22 -164.20 REMARK 500 ASP A 439 60.14 100.64 REMARK 500 HIS A 459 36.50 -80.40 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 259 145.73 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 133 22.5 L L OUTSIDE RANGE 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 A 776 DISTANCE = 5.27 ANGSTROMS 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 459 NE2 REMARK 620 2 HIS A 457 ND1 123.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 78 OE2 REMARK 620 2 HIS A 150 NE2 100.5 REMARK 620 3 HOH A 631 O 156.7 81.3 REMARK 620 4 GLU A 78 OE1 52.0 120.0 146.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 HIS A 460 NE2 96.0 REMARK 620 3 HOH A 785 O 79.0 117.2 REMARK 620 4 HIS A 458 ND1 117.3 75.2 159.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 842 A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4I0H RELATED DB: PDB REMARK 900 RELATED ID: 4I0I RELATED DB: PDB DBREF 4I0J A 57 453 UNP P56817 BACE1_HUMAN 57 453 SEQADV 4I0J MET A 56 UNP P56817 EXPRESSION TAG SEQADV 4I0J ARG A 454 UNP P56817 EXPRESSION TAG SEQADV 4I0J SER A 455 UNP P56817 EXPRESSION TAG SEQADV 4I0J HIS A 456 UNP P56817 EXPRESSION TAG SEQADV 4I0J HIS A 457 UNP P56817 EXPRESSION TAG SEQADV 4I0J HIS A 458 UNP P56817 EXPRESSION TAG SEQADV 4I0J HIS A 459 UNP P56817 EXPRESSION TAG SEQADV 4I0J HIS A 460 UNP P56817 EXPRESSION TAG SEQADV 4I0J HIS A 461 UNP P56817 EXPRESSION TAG SEQRES 1 A 406 MET ARG GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG SEQRES 2 A 406 GLY LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL SEQRES 3 A 406 GLY SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR SEQRES 4 A 406 GLY SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO SEQRES 5 A 406 PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR SEQRES 6 A 406 TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR SEQRES 7 A 406 GLN GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SEQRES 8 A 406 SER ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN SEQRES 9 A 406 ILE ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN SEQRES 10 A 406 GLY SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA SEQRES 11 A 406 GLU ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE SEQRES 12 A 406 ASP SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SEQRES 13 A 406 SER LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SEQRES 14 A 406 SER GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE SEQRES 15 A 406 GLY GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP SEQRES 16 A 406 TYR THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE SEQRES 17 A 406 ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET SEQRES 18 A 406 ASP CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SEQRES 19 A 406 SER GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE SEQRES 20 A 406 GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SER SER THR SEQRES 21 A 406 GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU SEQRES 22 A 406 VAL CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE SEQRES 23 A 406 PRO VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN SEQRES 24 A 406 GLN SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU SEQRES 25 A 406 ARG PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS SEQRES 26 A 406 TYR LYS PHE ALA ILE SER GLN SER SER THR GLY THR VAL SEQRES 27 A 406 MET GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE SEQRES 28 A 406 ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA SEQRES 29 A 406 CYS HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU SEQRES 30 A 406 GLY PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR SEQRES 31 A 406 ASN ILE PRO GLN THR ASP GLU SER ARG SER HIS HIS HIS SEQRES 32 A 406 HIS HIS HIS HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET 842 A 505 35 HETNAM ZN ZINC ION HETNAM 842 N-[(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-3-({1-[3- HETNAM 2 842 (1H-PYRAZOL-1-YL)PHENYL]CYCLOHEXYL}AMINO) HETNAM 3 842 PROPYL]ACETAMIDE FORMUL 2 ZN 4(ZN 2+) FORMUL 6 842 C27 H32 F2 N4 O2 FORMUL 7 HOH *225(H2 O) HELIX 1 1 SER A 59 VAL A 64 1 6 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 281 5 5 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 HELIX 14 14 THR A 450 HIS A 456 1 7 SHEET 1 A 9 ARG A 122 PRO A 131 0 SHEET 2 A 9 LYS A 136 SER A 147 -1 O LEU A 141 N LYS A 126 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 LYS A 70 -1 N ARG A 68 O TYR A 76 SHEET 5 A 9 SER A 230 ILE A 237 -1 O VAL A 231 N GLY A 69 SHEET 6 A 9 PHE A 211 LEU A 215 -1 N SER A 212 O ILE A 236 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 TRP A 250 O PHE A 415 SHEET 1 B13 ARG A 122 PRO A 131 0 SHEET 2 B13 LYS A 136 SER A 147 -1 O LEU A 141 N LYS A 126 SHEET 3 B13 VAL A 156 ASP A 167 -1 O GLU A 165 N GLU A 138 SHEET 4 B13 PHE A 99 GLY A 102 1 N PHE A 99 O ALA A 161 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 VAL A 77 O ILE A 90 SHEET 8 B13 LEU A 67 LYS A 70 -1 N ARG A 68 O TYR A 76 SHEET 9 B13 SER A 230 ILE A 237 -1 O VAL A 231 N GLY A 69 SHEET 10 B13 PHE A 211 LEU A 215 -1 N SER A 212 O ILE A 236 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 TRP A 250 O PHE A 415 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 361 N ILE A 344 SHEET 5 D 5 ALA A 430 VAL A 436 -1 O ALA A 430 N THR A 360 SHEET 1 E 3 VAL A 329 GLN A 332 0 SHEET 2 E 3 ASP A 378 PHE A 383 -1 O ASP A 379 N TRP A 331 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 2.07 SSBOND 2 CYS A 278 CYS A 443 1555 1555 2.08 SSBOND 3 CYS A 330 CYS A 380 1555 1555 2.05 LINK NE2 HIS A 459 ZN ZN A 501 1555 1555 1.96 LINK ND1 HIS A 457 ZN ZN A 501 1555 1555 1.98 LINK OE2 GLU A 78 ZN ZN A 503 1555 1555 2.02 LINK NE2 HIS A 150 ZN ZN A 503 1555 1555 2.09 LINK OD1 ASP A 192 ZN ZN A 502 1555 1555 2.17 LINK ZN ZN A 503 O HOH A 631 1555 1555 2.17 LINK NE2 HIS A 460 ZN ZN A 502 1555 1555 2.18 LINK ZN ZN A 502 O HOH A 785 1555 1555 2.38 LINK ND1 HIS A 458 ZN ZN A 502 1555 1555 2.44 LINK OE2 GLU A 165 ZN ZN A 504 1555 1555 2.64 LINK OE1 GLU A 78 ZN ZN A 503 1555 1555 2.64 CISPEP 1 SER A 83 PRO A 84 0 -5.19 CISPEP 2 ARG A 189 PRO A 190 0 7.47 CISPEP 3 TYR A 283 ASP A 284 0 4.79 CISPEP 4 GLY A 433 PRO A 434 0 -1.78 SITE 1 AC1 4 GLU A 316 ASP A 451 HIS A 457 HIS A 459 SITE 1 AC2 5 ASP A 192 HIS A 458 HIS A 460 HOH A 636 SITE 2 AC2 5 HOH A 785 SITE 1 AC3 5 GLU A 78 HIS A 110 HIS A 150 ASN A 175 SITE 2 AC3 5 HOH A 631 SITE 1 AC4 3 GLU A 138 GLU A 165 HOH A 709 SITE 1 AC5 16 LEU A 91 ASP A 93 GLY A 95 PRO A 131 SITE 2 AC5 16 TYR A 132 THR A 133 GLY A 135 PHE A 169 SITE 3 AC5 16 ILE A 171 TRP A 176 ILE A 187 TYR A 259 SITE 4 AC5 16 ASP A 289 GLY A 291 THR A 390 HOH A 607 CRYST1 75.228 104.039 99.063 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 0.013293 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010095 0.00000