HEADER HYDROLASE 04-AUG-04 1W50 TITLE APO STRUCTURE OF BACE (BETA SECRETASE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ACTIVE PROTEASE DOMAIN, RESIDUES 43-453; COMPND 5 SYNONYM: BETA-SITE APP CLEAVING ENZYME 1, BETA-SITE AMYLOID PRECURSOR COMPND 6 PROTEIN CLEAVING ENZYME 1, ASPARTYL PROTEASE 2, ASP2, MEMBRANE- COMPND 7 ASSOCIATED ASPARTIC PROTEASE 2, MEMAPSIN-2; COMPND 8 EC: 3.4.23.46; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS ALTERNATIVE SPLICING, ALZHEIMER'S DISEASE, ASPARTIC PROTEASE, KEYWDS 2 ASPARTYL PROTEASE, BASE, BETA-SECRETASE, GLYCOPROTEIN, HYDROLASE, KEYWDS 3 MEMAPSIN 2, TRANSMEMBRANE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR S.PATEL,L.VUILLARD,A.CLEASBY,C.W.MURRAY,J.YON REVDAT 4 13-DEC-23 1W50 1 REMARK REVDAT 3 24-FEB-09 1W50 1 VERSN REVDAT 2 30-SEP-04 1W50 1 JRNL REVDAT 1 23-SEP-04 1W50 0 JRNL AUTH S.PATEL,L.VUILLARD,A.CLEASBY,C.W.MURRAY,J.YON JRNL TITL APO AND INHIBITOR COMPLEX STRUCTURES OF BACE JRNL TITL 2 (BETA-SECRETASE) JRNL REF J.MOL.BIOL. V. 343 407 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15451669 JRNL DOI 10.1016/J.JMB.2004.08.018 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.29 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 48964 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2624 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3586 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 201 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2966 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.53000 REMARK 3 B22 (A**2) : -0.53000 REMARK 3 B33 (A**2) : 0.79000 REMARK 3 B12 (A**2) : -0.26000 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.063 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3018 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2677 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4107 ; 1.427 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6211 ; 0.840 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 375 ; 7.215 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 451 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3387 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 637 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 631 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3270 ; 0.240 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1784 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 229 ; 0.218 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 15 ; 0.221 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 63 ; 0.290 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.181 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1870 ; 2.943 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3020 ; 4.075 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1148 ; 3.752 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1087 ; 5.221 ; 7.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. THIS ENTRY CONTAINS SOME ATOMS WHICH HAVE BEEN REMARK 3 REFINED WITH AN OCCUPANCY OF 0.00. RESIDUES BETWEEN 157 AND 169 REMARK 3 WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS REMARK 4 REMARK 4 1W50 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1290020659. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51594 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 39.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1FKN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.60 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 56.36933 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 112.73867 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 84.55400 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 140.92333 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 28.18467 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 56.36933 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 112.73867 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 140.92333 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 84.55400 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 28.18467 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 RESIDUES 56 AND 57 MUTATED TO LYS FROM ARGININE. REMARK 400 THE MUTATION IS NOT VISIBLE IN THE STRUCTURE REMARK 400 DEPOSITED. REMARK 400 REMARK 400 FUNCTION: RESPONSIBLE FOR THE PROTEOLYTIC PROCESSING OF REMARK 400 THE AMYLOID PRECURSOR PROTEIN (APP). 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 LEU A -18 REMARK 465 PRO A -17 REMARK 465 ARG A -16 REMARK 465 GLU A -15 REMARK 465 THR A -14 REMARK 465 ASP A -13 REMARK 465 GLU A -12 REMARK 465 GLU A -11 REMARK 465 PRO A -10 REMARK 465 GLU A -9 REMARK 465 GLU A -8 REMARK 465 PRO A -7 REMARK 465 GLY A -6 REMARK 465 LYS A -5 REMARK 465 LYS A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 GLY A 158 REMARK 465 PHE A 159 REMARK 465 PRO A 160 REMARK 465 LEU A 161 REMARK 465 ASN A 162 REMARK 465 GLN A 163 REMARK 465 SER A 164 REMARK 465 GLU A 165 REMARK 465 VAL A 166 REMARK 465 LEU A 167 REMARK 465 PRO A 387 REMARK 465 GLN A 388 REMARK 465 THR A 389 REMARK 465 ASP A 390 REMARK 465 GLU A 391 REMARK 465 SER A 392 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 ILE A 386 CA C O CB CG1 CG2 CD1 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 GLU A 1 CG CD OE1 OE2 REMARK 480 ARG A 7 NE CZ NH1 NH2 REMARK 480 ARG A 64 NE CZ NH1 NH2 REMARK 480 LYS A 107 CE NZ REMARK 480 LYS A 142 NZ REMARK 480 GLN A 266 CG CD OE1 NE2 REMARK 480 GLN A 271 CG CD OE1 NE2 REMARK 480 ASP A 381 CG OD1 OD2 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 GLY A 330 O HOH A 2254 1.95 REMARK 500 O HOH A 2084 O HOH A 2166 2.15 REMARK 500 CG PRO A 258 OE1 GLN A 266 2.16 REMARK 500 O HOH A 2052 O HOH A 2137 2.16 REMARK 500 C PRO A 281 O HOH A 2226 2.18 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 GLU A 1 CB GLU A 1 CG -0.335 REMARK 500 ARG A 7 CD ARG A 7 NE -0.174 REMARK 500 ARG A 64 CD ARG A 64 NE 0.230 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 7 CG - CD - NE ANGL. DEV. = 16.3 DEGREES REMARK 500 ARG A 7 CD - NE - CZ ANGL. DEV. = 12.5 DEGREES REMARK 500 ASP A 32 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 64 CD - NE - CZ ANGL. DEV. = -13.2 DEGREES REMARK 500 ASP A 138 CB - CG - OD2 ANGL. DEV. = 6.0 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 GLN A 73 22.97 -141.93 REMARK 500 HIS A 89 47.61 -100.94 REMARK 500 PHE A 108 -63.13 -104.72 REMARK 500 ALA A 122 -169.55 -77.39 REMARK 500 CYS A 155 -70.12 -101.69 REMARK 500 TRP A 197 -86.74 -136.38 REMARK 500 ASN A 209 -13.45 71.97 REMARK 500 ASP A 216 117.45 -36.19 REMARK 500 GLU A 310 -78.94 -56.27 REMARK 500 ASP A 363 -130.00 -160.95 REMARK 500 PHE A 365 -75.44 -76.71 REMARK 500 ASN A 385 -60.87 -104.38 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 A2016 DISTANCE = 6.22 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FKN RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-SECRETASE COMPLEXED WITH INHIBITOR REMARK 900 RELATED ID: 1M4H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED WITHINHIBITOR OM00-3 REMARK 900 RELATED ID: 1PY1 RELATED DB: PDB REMARK 900 COMPLEX OF GGA1-VHS DOMAIN AND BETA- SECRETASE C- REMARK 900 TERMINALPHOSPHOPEPTIDE REMARK 900 RELATED ID: 1SGZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UNBOUND BETA-SECRETASE CATALYTICDOMAIN. REMARK 900 RELATED ID: 1UJJ RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C -TERMINAL PEPTIDEFROM BACE REMARK 900 RELATED ID: 1UJK RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C -TERMINALPHOSPHOPEPTIDE REMARK 900 FROM BACE REMARK 900 RELATED ID: 1W51 RELATED DB: PDB REMARK 900 BACE (BETA SECRETASE) IN COMPLEX WITH A NANOMOLAR NON-PEPTIDIC REMARK 900 INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 56 AND 57 FROM THE UNIPROT REFERENCE BELOW HAVE REMARK 999 HAVE BEEN MUTATED TO LYS FROM ARG. SINCE THIS MUTATION IS REMARK 999 NOT VISIBLE IN THE STRUCTURE, THERE ARE NO SEQADV RECORDS REMARK 999 GIVEN BELOW. DBREF 1W50 A -18 392 UNP P56817 BAE1_HUMAN 43 453 SEQRES 1 A 411 LEU PRO ARG GLU THR ASP GLU GLU PRO GLU GLU PRO GLY SEQRES 2 A 411 LYS LYS GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG SEQRES 3 A 411 GLY LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL SEQRES 4 A 411 GLY SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR SEQRES 5 A 411 GLY SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO SEQRES 6 A 411 PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR SEQRES 7 A 411 TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR SEQRES 8 A 411 GLN GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SEQRES 9 A 411 SER ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN SEQRES 10 A 411 ILE ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN SEQRES 11 A 411 GLY SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA SEQRES 12 A 411 GLU ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE SEQRES 13 A 411 ASP SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SEQRES 14 A 411 SER LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SEQRES 15 A 411 SER GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE SEQRES 16 A 411 GLY GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP SEQRES 17 A 411 TYR THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE SEQRES 18 A 411 ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET SEQRES 19 A 411 ASP CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SEQRES 20 A 411 SER GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE SEQRES 21 A 411 GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SER SER THR SEQRES 22 A 411 GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU SEQRES 23 A 411 VAL CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE SEQRES 24 A 411 PRO VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN SEQRES 25 A 411 GLN SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU SEQRES 26 A 411 ARG PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS SEQRES 27 A 411 TYR LYS PHE ALA ILE SER GLN SER SER THR GLY THR VAL SEQRES 28 A 411 MET GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE SEQRES 29 A 411 ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA SEQRES 30 A 411 CYS HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU SEQRES 31 A 411 GLY PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR SEQRES 32 A 411 ASN ILE PRO GLN THR ASP GLU SER HET IOD A1502 1 HET IOD A1503 1 HET IOD A1504 1 HET IOD A1505 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 4(I 1-) FORMUL 6 HOH *279(H2 O) HELIX 1 1 GLN A 53 SER A 57 5 5 HELIX 2 2 TYR A 123 ALA A 127 5 5 HELIX 3 3 PRO A 135 THR A 144 1 10 HELIX 4 4 ASP A 180 SER A 182 5 3 HELIX 5 5 ASP A 216 TYR A 222 5 7 HELIX 6 6 LYS A 238 SER A 252 1 15 HELIX 7 7 PRO A 258 LEU A 263 1 6 HELIX 8 8 PRO A 276 PHE A 280 5 5 HELIX 9 9 LEU A 301 TYR A 305 1 5 HELIX 10 10 GLY A 334 GLU A 339 1 6 HELIX 11 11 ARG A 347 ARG A 349 5 3 HELIX 12 12 MET A 379 GLY A 383 5 5 SHEET 1 AA 3 ARG A 61 PRO A 70 0 SHEET 2 AA 3 LYS A 75 SER A 86 -1 O TRP A 76 N VAL A 69 SHEET 3 AA 3 TYR A 14 VAL A 20 -1 O THR A 19 N SER A 86 SHEET 1 AB 7 ARG A 61 PRO A 70 0 SHEET 2 AB 7 LYS A 75 SER A 86 -1 O TRP A 76 N VAL A 69 SHEET 3 AB 7 VAL A 95 ASP A 106 -1 O VAL A 95 N VAL A 85 SHEET 4 AB 7 PHE A 38 GLY A 41 1 O PHE A 38 N ALA A 100 SHEET 5 AB 7 GLY A 117 GLY A 120 -1 O ILE A 118 N ALA A 39 SHEET 6 AB 7 GLN A 25 ASP A 32 1 O LEU A 30 N LEU A 119 SHEET 7 AB 7 TYR A 14 VAL A 20 -1 O TYR A 14 N VAL A 31 SHEET 1 AC 5 GLN A 211 ASP A 212 0 SHEET 2 AC 5 ILE A 203 ILE A 208 -1 O ILE A 208 N GLN A 211 SHEET 3 AC 5 ILE A 283 MET A 288 -1 O SER A 284 N GLU A 207 SHEET 4 AC 5 GLN A 294 ILE A 300 -1 O PHE A 296 N LEU A 287 SHEET 5 AC 5 ALA A 369 VAL A 375 -1 O ALA A 369 N THR A 299 SHEET 1 AD 4 SER A 225 VAL A 227 0 SHEET 2 AD 4 THR A 331 MET A 333 1 O THR A 331 N ILE A 226 SHEET 3 AD 4 LEU A 234 PRO A 237 -1 O ARG A 235 N VAL A 332 SHEET 4 AD 4 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 SHEET 1 AE 3 VAL A 268 TRP A 270 0 SHEET 2 AE 3 ASP A 318 PHE A 322 -1 O ASP A 318 N TRP A 270 SHEET 3 AE 3 LEU A 306 PRO A 308 -1 O ARG A 307 N LYS A 321 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.07 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.04 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.05 CISPEP 1 SER A 22 PRO A 23 0 -3.14 CISPEP 2 ARG A 128 PRO A 129 0 6.06 CISPEP 3 TYR A 222 ASP A 223 0 -4.55 CISPEP 4 GLY A 372 PRO A 373 0 -7.82 SITE 1 AC1 1 SER A 105 SITE 1 AC2 3 LYS A 107 HOH A2121 HOH A2122 SITE 1 AC3 2 ARG A 96 GLU A 134 SITE 1 AC4 1 HOH A2088 CRYST1 103.243 103.243 169.108 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 0.009686 0.005592 0.000000 0.00000 SCALE2 0.000000 0.011184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005913 0.00000