HEADER HYDROLASE 10-NOV-16 5MCQ TITLE CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH ACTIVE SITE AND EXOSITE TITLE 2 BINDING PEPTIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASPARTYL PROTEASE 2,ASP 2,BETA-SITE AMYLOID PRECURSOR COMPND 5 PROTEIN CLEAVING ENZYME 1,BETA-SITE APP CLEAVING ENZYME 1,MEMAPSIN-2, COMPND 6 MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; COMPND 7 EC: 3.4.23.46; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: BACE-1 ACTIVE AND EXOSITE BINDING INHIBITOR; COMPND 11 CHAIN: D; COMPND 12 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS PROTEASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, HYDROLASE, KEYWDS 2 EXOSITE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUGLSTATTER,M.STIHLE,J.BENZ REVDAT 4 23-OCT-24 5MCQ 1 REMARK REVDAT 3 01-MAY-24 5MCQ 1 REMARK REVDAT 2 01-NOV-17 5MCQ 1 JRNL REVDAT 1 27-SEP-17 5MCQ 0 JRNL AUTH N.RUDERISCH,D.SCHLATTER,A.KUGLSTATTER,W.GUBA,S.HUBER, JRNL AUTH 2 C.CUSULIN,J.BENZ,A.C.RUFER,J.HOERNSCHEMEYER,C.SCHWEITZER, JRNL AUTH 3 T.BULAU,A.GARTNER,E.HOFFMANN,J.NIEWOEHNER,C.PATSCH, JRNL AUTH 4 K.BAUMANN,H.LOETSCHER,E.KITAS,P.O.FRESKGARD JRNL TITL POTENT AND SELECTIVE BACE-1 PEPTIDE INHIBITORS LOWER BRAIN A JRNL TITL 2 BETA LEVELS MEDIATED BY BRAIN SHUTTLE TRANSPORT. JRNL REF EBIOMEDICINE V. 24 76 2017 JRNL REFN ESSN 2352-3964 JRNL PMID 28923680 JRNL DOI 10.1016/J.EBIOM.2017.09.004 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 59801 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3169 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4317 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE SET COUNT : 246 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3248 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 586 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -1.65000 REMARK 3 B12 (A**2) : 0.25000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.825 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3389 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4598 ; 1.932 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 422 ; 6.990 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;36.190 ;23.935 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 525 ;14.250 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.696 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2594 ; 0.013 ; 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): 1675 ; 2.922 ; 2.904 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2088 ; 4.347 ; 4.334 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1713 ; 4.197 ; 3.193 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): 5835 ; 9.087 ;26.593 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 : NULL 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 5MCQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63008 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 48.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.24 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08130 REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.13 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: UNPUBLISHED STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MAGNESIUM ACETATE, 0.1M SODIUM REMARK 280 ACETATE, 8% (W/V) PEG8000, PH 4.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 77.56667 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 38.78333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 38.78333 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 77.56667 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 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 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 N ASN A 175 O HOH A 601 2.15 REMARK 500 O HOH A 862 O HOH A 1025 2.16 REMARK 500 N ASN A 175 O HOH A 601 2.18 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 1127 O HOH A 1127 5554 1.51 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 DLY D 664 N DLY D 664 CA -0.122 REMARK 500 DLY D 664 CA DLY D 664 CB -0.181 REMARK 500 DLY D 666 CA DLY D 666 CB -0.193 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 157 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 157 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 256 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 296 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 296 NE - CZ - NH2 ANGL. DEV. = 5.6 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 169 -65.08 -102.79 REMARK 500 TRP A 258 -83.40 -139.15 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 GLY D 665 DLY D 666 -149.49 REMARK 500 STA D 671 VAL D 672 -116.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 STA D 671 34.97 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 A1148 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1149 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A1150 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH A1151 DISTANCE = 8.84 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues STA D 671 REMARK 800 through VAL D 672 bound to ASN D 670 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5MBW RELATED DB: PDB REMARK 900 RELATED ID: 5MCO RELATED DB: PDB DBREF 5MCQ A 46 454 UNP P56817 BACE1_HUMAN 46 454 DBREF 5MCQ D 655 676 PDB 5MCQ 5MCQ 655 676 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 LYS 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 SEQRES 1 D 22 GLY GLY GLY TYR PRO TYR PHE ILE PRO DLY GLY DLY GLY SEQRES 2 D 22 GLU VAL ASN STA VAL ALA GLU DPR NH2 HET DLY D 664 9 HET DLY D 666 9 HET STA D 671 11 HET DPR D 675 7 HET NH2 D 676 1 HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HETNAM DLY D-LYSINE HETNAM STA STATINE HETNAM DPR D-PROLINE HETNAM NH2 AMINO GROUP HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DLY 2(C6 H14 N2 O2) FORMUL 2 STA C8 H17 N O3 FORMUL 2 DPR C5 H9 N O2 FORMUL 2 NH2 H2 N FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 HOH *586(H2 O) HELIX 1 AA1 SER A 59 VAL A 64 1 6 HELIX 2 AA2 GLN A 114 SER A 118 5 5 HELIX 3 AA3 TYR A 184 ALA A 188 5 5 HELIX 4 AA4 PRO A 196 THR A 205 1 10 HELIX 5 AA5 ALA A 218 PHE A 220 5 3 HELIX 6 AA6 ASP A 241 SER A 243 5 3 HELIX 7 AA7 ASP A 277 TYR A 283 5 7 HELIX 8 AA8 LYS A 299 SER A 314 1 16 HELIX 9 AA9 PRO A 319 LEU A 324 1 6 HELIX 10 AB1 PRO A 337 PHE A 341 5 5 HELIX 11 AB2 LEU A 362 TYR A 366 1 5 HELIX 12 AB3 GLY A 395 GLU A 400 1 6 HELIX 13 AB4 ASP A 439 GLY A 444 5 6 SHEET 1 AA1 9 ARG A 122 PRO A 131 0 SHEET 2 AA1 9 LYS A 136 SER A 147 -1 O LEU A 141 N LYS A 126 SHEET 3 AA1 9 TYR A 75 VAL A 81 -1 N THR A 80 O SER A 147 SHEET 4 AA1 9 LEU A 67 LYS A 70 -1 N ARG A 68 O TYR A 76 SHEET 5 AA1 9 SER A 230 ILE A 237 -1 O GLY A 233 N LEU A 67 SHEET 6 AA1 9 PHE A 211 GLY A 217 -1 N GLN A 214 O SER A 234 SHEET 7 AA1 9 PHE A 402 ASP A 407 -1 O VAL A 404 N LEU A 213 SHEET 8 AA1 9 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403 SHEET 9 AA1 9 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413 SHEET 1 AA213 ARG A 122 PRO A 131 0 SHEET 2 AA213 LYS A 136 SER A 147 -1 O LEU A 141 N LYS A 126 SHEET 3 AA213 VAL A 156 ASP A 167 -1 O ALA A 162 N GLU A 140 SHEET 4 AA213 PHE A 99 GLY A 102 1 N VAL A 101 O ILE A 163 SHEET 5 AA213 GLY A 178 GLY A 181 -1 O ILE A 179 N ALA A 100 SHEET 6 AA213 GLN A 86 ASP A 93 1 N LEU A 91 O LEU A 180 SHEET 7 AA213 TYR A 75 VAL A 81 -1 N TYR A 75 O VAL A 92 SHEET 8 AA213 LEU A 67 LYS A 70 -1 N ARG A 68 O TYR A 76 SHEET 9 AA213 SER A 230 ILE A 237 -1 O GLY A 233 N LEU A 67 SHEET 10 AA213 PHE A 211 GLY A 217 -1 N GLN A 214 O SER A 234 SHEET 11 AA213 PHE A 402 ASP A 407 -1 O VAL A 404 N LEU A 213 SHEET 12 AA213 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403 SHEET 13 AA213 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413 SHEET 1 AA3 5 GLN A 272 ASP A 273 0 SHEET 2 AA3 5 ILE A 264 ILE A 269 -1 N ILE A 269 O GLN A 272 SHEET 3 AA3 5 ILE A 344 MET A 349 -1 O TYR A 347 N ARG A 266 SHEET 4 AA3 5 GLN A 355 ILE A 361 -1 O ILE A 361 N ILE A 344 SHEET 5 AA3 5 ALA A 430 VAL A 436 -1 O ALA A 430 N THR A 360 SHEET 1 AA4 4 SER A 286 VAL A 288 0 SHEET 2 AA4 4 THR A 392 MET A 394 1 O MET A 394 N ILE A 287 SHEET 3 AA4 4 LEU A 295 PRO A 298 -1 N ARG A 296 O VAL A 393 SHEET 4 AA4 4 ILE A 385 SER A 388 1 O SER A 386 N LEU A 297 SHEET 1 AA5 4 LEU A 367 VAL A 370 0 SHEET 2 AA5 4 ASP A 378 PHE A 383 -1 O CYS A 380 N VAL A 370 SHEET 3 AA5 4 GLN A 327 GLN A 332 -1 N TRP A 331 O ASP A 379 SHEET 4 AA5 4 TYR D 660 PRO D 663 -1 O TYR D 660 N CYS A 330 SSBOND 1 CYS A 216 CYS A 420 1555 1555 2.17 SSBOND 2 CYS A 278 CYS A 443 1555 1555 2.14 SSBOND 3 CYS A 330 CYS A 380 1555 1555 2.16 LINK C PRO D 663 N DLY D 664 1555 1555 1.32 LINK C DLY D 664 N GLY D 665 1555 1555 1.32 LINK C GLY D 665 N DLY D 666 1555 1555 1.34 LINK C DLY D 666 N GLY D 667 1555 1555 1.33 LINK C ASN D 670 N STA D 671 1555 1555 1.34 LINK C STA D 671 N VAL D 672 1555 1555 1.32 LINK C GLU D 674 N DPR D 675 1555 1555 1.34 LINK C DPR D 675 N NH2 D 676 1555 1555 1.31 CISPEP 1 SER A 83 PRO A 84 0 -6.14 CISPEP 2 ARG A 189 PRO A 190 0 1.36 CISPEP 3 TYR A 283 ASP A 284 0 2.15 CISPEP 4 GLY A 433 PRO A 434 0 0.09 CISPEP 5 TYR D 658 PRO D 659 0 -2.49 SITE 1 AC1 4 ARG A 111 TYR A 112 GLN A 114 HOH A 851 SITE 1 AC2 5 SER A 59 PHE A 60 GLU A 165 HOH A 975 SITE 2 AC2 5 HOH A1005 SITE 1 AC3 5 ARG A 157 ASN A 159 GLU A 195 SER A 200 SITE 2 AC3 5 HOH A 729 SITE 1 AC4 2 GLU A 226 HOH A 844 SITE 1 AC5 14 ASP A 93 GLY A 95 SER A 96 PRO A 131 SITE 2 AC5 14 TYR A 132 THR A 133 GLN A 134 ILE A 187 SITE 3 AC5 14 TYR A 259 ASP A 289 GLY A 291 ASN D 670 SITE 4 AC5 14 ALA D 673 GLU D 674 CRYST1 101.930 101.930 116.350 90.00 90.00 120.00 P 32 2 1 6 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 0.009811 0.005664 0.000000 0.00000 SCALE2 0.000000 0.011328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008595 0.00000