PDB Short entry for 4GMI HEADER HYDROLASE/HYDROLASE INHIBITOR 16-AUG-12 4GMI TITLE BACE-1 IN COMPLEX WITH HEA-TYPE MACROCYCLIC INHIBITOR, MV078571 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 57-446; 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS BACE-1, ASP2, BACE, MACROCYCLE, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.D.LINDBERG,D.DERBYSHIRE REVDAT 1 04-SEP-13 4GMI 0 JRNL AUTH V.SANDGREN,O.BELDA,P.O.JOHANSSON,I.KVARNSTROM,J.LINDBERG, JRNL AUTH 2 A.DAHLGREN,B.SAMUELSSON JRNL TITL DESIGN AND SYNTHESIS OF NOVEL BACE-1 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 34459 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1729 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1566 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.970 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3340 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4594 ; 2.186 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 437 ; 6.724 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;35.095 ;24.110 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 531 ;13.013 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;14.267 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 499 ; 0.170 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2614 ; 0.012 ; 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): 2013 ; 1.356 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3294 ; 2.219 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1327 ; 3.310 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1282 ; 5.220 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -3 A 385 REMARK 3 ORIGIN FOR THE GROUP (A): 2.2094 1.3897 14.8653 REMARK 3 T TENSOR REMARK 3 T11: 0.0036 T22: 0.0067 REMARK 3 T33: 0.0362 T12: 0.0022 REMARK 3 T13: -0.0005 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.2173 L22: 0.3049 REMARK 3 L33: 0.7854 L12: 0.0806 REMARK 3 L13: -0.0755 L23: 0.0141 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: -0.0183 S13: -0.0224 REMARK 3 S21: -0.0016 S22: -0.0067 S23: 0.0008 REMARK 3 S31: 0.0141 S32: 0.0528 S33: -0.0070 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 4GMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-12. REMARK 100 THE RCSB ID CODE IS RCSB074369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-11 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34506 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.798 REMARK 200 RESOLUTION RANGE LOW (A) : 61.742 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : 0.21000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 1000, 0.1 NA-ACETATE, 5% REMARK 280 GLYCEROL , PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 24.07950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.06750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.33600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.06750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.07950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.33600 REMARK 290 SMTRY3 4 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 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 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 -5 REMARK 465 ARG A -4 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 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 LEU A 167 CG CD1 CD2 REMARK 470 LEU A 377 CG CD1 CD2 REMARK 470 ASN A 385 CB CG OD1 ND2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 7 CG CD NE CZ NH1 NH2 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 CB SER A 113 O HOH A 824 2.15 REMARK 500 OD2 ASP A 259 O HOH A 777 2.16 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 NZ LYS A 350 O HOH A 818 3555 2.02 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 PHE A 108 CE2 PHE A 108 CD2 0.123 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 ASP A 62 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 130 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 194 NE - CZ - NH1 ANGL. DEV. = -3.1 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 108 -60.69 -106.49 REMARK 500 TRP A 197 -92.98 -140.95 REMARK 500 ASN A 209 54.72 35.76 REMARK 500 ASP A 311 115.18 -164.93 REMARK 500 ALA A 323 43.05 -99.41 REMARK 500 CYS A 359 54.93 -98.99 REMARK 500 ASP A 363 -162.03 -124.87 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 0XA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DPF RELATED DB: PDB REMARK 900 RELATED ID: 4DPI RELATED DB: PDB DBREF 4GMI A -4 385 UNP P56817 BACE1_HUMAN 57 446 SEQADV 4GMI MET A -5 UNP P56817 INITIATING METHIONINE SEQRES 1 A 391 MET ARG GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG SEQRES 2 A 391 GLY LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL SEQRES 3 A 391 GLY SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR SEQRES 4 A 391 GLY SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO SEQRES 5 A 391 PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR SEQRES 6 A 391 TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR SEQRES 7 A 391 GLN GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SEQRES 8 A 391 SER ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN SEQRES 9 A 391 ILE ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN SEQRES 10 A 391 GLY SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA SEQRES 11 A 391 GLU ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE SEQRES 12 A 391 ASP SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SEQRES 13 A 391 SER LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SEQRES 14 A 391 SER GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE SEQRES 15 A 391 GLY GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP SEQRES 16 A 391 TYR THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE SEQRES 17 A 391 ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET SEQRES 18 A 391 ASP CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SEQRES 19 A 391 SER GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE SEQRES 20 A 391 GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SER SER THR SEQRES 21 A 391 GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU SEQRES 22 A 391 VAL CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE SEQRES 23 A 391 PRO VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN SEQRES 24 A 391 GLN SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU SEQRES 25 A 391 ARG PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS SEQRES 26 A 391 TYR LYS PHE ALA ILE SER GLN SER SER THR GLY THR VAL SEQRES 27 A 391 MET GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE SEQRES 28 A 391 ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA SEQRES 29 A 391 CYS HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU SEQRES 30 A 391 GLY PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR SEQRES 31 A 391 ASN HET 0XA A 401 74 HET ACT A 402 4 HET GOL A 403 6 HETNAM 0XA (4S,8E)-4-[(1R)-2-{[2-(5-TERT-BUTYL-1,3-OXAZOL-2-YL) HETNAM 2 0XA PROPAN-2-YL]AMINO}-1-HYDROXYETHYL]-16-METHYL-6-OXA-3- HETNAM 3 0XA AZABICYCLO[12.3.1]OCTADECA-1(18),8,14,16-TETRAENE-2, HETNAM 4 0XA 13-DIONE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 0XA C29 H41 N3 O5 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *330(H2 O) HELIX 1 1 SER A -2 VAL A 3 1 6 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 TYR A 222 5 7 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 ASP A 311 SER A 315 5 5 HELIX 12 12 GLY A 334 GLU A 339 1 6 HELIX 13 13 ARG A 347 ARG A 349 5 3 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 TYR A 14 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 SER A 169 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 VAL A 343 N LEU A 152 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 THR A 94 ASP A 106 -1 O VAL A 95 N VAL A 85 SHEET 4 B13 PHE A 38 GLY A 41 1 N VAL A 40 O ALA A 100 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 TYR A 14 VAL A 20 -1 N MET A 18 O LEU A 27 SHEET 8 B13 LEU A 6 LYS A 9 -1 N ARG A 7 O TYR A 15 SHEET 9 B13 SER A 169 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 VAL A 343 N LEU A 152 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 SER A 284 N GLU A 207 SHEET 4 D 5 GLN A 294 ILE A 300 -1 O ILE A 298 N LEU A 285 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 2.15 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.11 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.12 CISPEP 1 SER A 22 PRO A 23 0 -3.46 CISPEP 2 ARG A 128 PRO A 129 0 0.34 CISPEP 3 TYR A 222 ASP A 223 0 1.01 CISPEP 4 GLY A 372 PRO A 373 0 1.39 SITE 1 AC1 17 GLN A 12 LEU A 30 ASP A 32 GLY A 34 SITE 2 AC1 17 SER A 35 PRO A 70 TYR A 71 THR A 72 SITE 3 AC1 17 GLN A 73 TYR A 198 ILE A 226 ASP A 228 SITE 4 AC1 17 GLY A 230 THR A 232 ACT A 402 HOH A 611 SITE 5 AC1 17 HOH A 620 SITE 1 AC2 6 THR A 72 TYR A 198 LYS A 224 0XA A 401 SITE 2 AC2 6 HOH A 545 HOH A 580 SITE 1 AC3 4 SER A 187 LEU A 188 TRP A 189 HOH A 822 CRYST1 48.159 76.672 104.135 90.00 90.00 90.00 P 21 21 21 4 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 0.020765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009603 0.00000