PDB Short entry for 3MSL HEADER HYDROLASE/HYDROLASE INHIBITOR 29-APR-10 3MSL TITLE FRAGMENT BASED DISCOVERY AND OPTIMISATION OF BACE-1 INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 48-453; COMPND 5 SYNONYM: BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA- COMPND 6 SITE APP CLEAVING ENZYME 1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2, COMPND 7 MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2; 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: BACE, BACE1, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS PROTEASE, ALZHEIMER'S DISEASE, ASPARTIC PROTEASE, ASPARTYL PROTEASE, KEYWDS 2 BASE, BETA-SECRETASE, GLYCOPROTEIN, HYDROLASE, MEMAPSIN 2, AMYLOID KEYWDS 3 PRECURSOR PROTEIN SECRETASES, ASPARTIC ENDOPEPTIDASES, FRAGMENT- KEYWDS 4 BASED DRUG DESIGN, FLUORESCENCE POLARISATION, TRANSMEMBRANE, KEYWDS 5 ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.SMITH,J.MADDEN,J.BARKER REVDAT 4 06-SEP-23 3MSL 1 REMARK SEQADV REVDAT 3 25-MAY-11 3MSL 1 HEADER REVDAT 2 01-SEP-10 3MSL 1 JRNL REVDAT 1 14-JUL-10 3MSL 0 JRNL AUTH J.MADDEN,J.R.DOD,R.GODEMANN,J.KRAEMER,M.SMITH, JRNL AUTH 2 M.BINISZKIEWICZ,D.J.HALLETT,J.BARKER,J.D.DYEKJAER, JRNL AUTH 3 T.HESTERKAMP JRNL TITL FRAGMENT-BASED DISCOVERY AND OPTIMIZATION OF BACE1 JRNL TITL 2 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 5329 2010 JRNL REFN ISSN 0960-894X JRNL PMID 20656487 JRNL DOI 10.1016/J.BMCL.2010.06.089 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 3 NUMBER OF REFLECTIONS : 17067 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 870 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1271 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2965 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 1.09000 REMARK 3 B12 (A**2) : -0.36000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.165 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.199 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3044 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4143 ; 1.036 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 375 ; 5.434 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;31.790 ;23.881 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;13.727 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.170 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 453 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2329 ; 0.003 ; 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): 1869 ; 0.328 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3019 ; 0.590 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1175 ; 0.184 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1124 ; 0.332 ; 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6464 -40.8946 -0.6597 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.0271 REMARK 3 T33: 0.0024 T12: 0.0036 REMARK 3 T13: -0.0060 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.7903 L22: 0.5553 REMARK 3 L33: 0.5429 L12: 0.3330 REMARK 3 L13: 0.4554 L23: 0.3606 REMARK 3 S TENSOR REMARK 3 S11: 0.0033 S12: 0.0520 S13: 0.0022 REMARK 3 S21: 0.0273 S22: 0.0064 S23: -0.0065 REMARK 3 S31: -0.0005 S32: 0.0354 S33: -0.0097 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 3MSL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000058945. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL 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 : 17067 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 61.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 200 DATA REDUNDANCY : 11.89 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : 0.10600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 11.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : 0.13100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 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: PDB ENTRY 1W50 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 5000MME 180MM AMMONIUM IODIDE REMARK 280 AND 180MM SODIUM CITRATE PH6.6 , VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 273K 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 57.61333 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 115.22667 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 86.42000 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 144.03333 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 28.80667 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 57.61333 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 115.22667 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 144.03333 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 86.42000 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 28.80667 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 GLY A -15 REMARK 465 PRO 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 ARG A -5 REMARK 465 ARG 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 ILE A 386 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 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: 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 ARG A 7 CD ARG A 7 NE -0.308 REMARK 500 LYS A 107 CD LYS A 107 CE -0.286 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 LYS A 75 N - CA - C ANGL. DEV. = -17.9 DEGREES REMARK 500 LYS A 107 CD - CE - NZ ANGL. DEV. = 14.9 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 TYR A 71 -144.81 -140.84 REMARK 500 THR A 72 -77.73 -72.09 REMARK 500 HIS A 89 49.17 -104.21 REMARK 500 TRP A 197 -80.54 -150.08 REMARK 500 LYS A 224 147.79 -179.09 REMARK 500 THR A 274 118.54 -162.63 REMARK 500 THR A 275 90.43 100.31 REMARK 500 GLU A 310 -74.20 -44.52 REMARK 500 VAL A 312 60.72 -111.80 REMARK 500 ALA A 313 23.27 -78.04 REMARK 500 THR A 314 97.43 178.96 REMARK 500 SER A 315 101.38 124.09 REMARK 500 GLN A 316 -85.17 -93.26 REMARK 500 ASP A 317 -134.28 16.54 REMARK 500 ASP A 318 -67.68 -103.13 REMARK 500 CYS A 319 138.14 60.06 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 IOD A 393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 394 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EV5 A 395 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MSJ RELATED DB: PDB REMARK 900 RELATED ID: 3MSK RELATED DB: PDB REMARK 900 RELATED ID: 3MSM RELATED DB: PDB DBREF 3MSL A -13 392 UNP P56817 BACE1_HUMAN 48 453 SEQADV 3MSL GLY A -15 UNP P56817 EXPRESSION TAG SEQADV 3MSL PRO A -14 UNP P56817 EXPRESSION TAG SEQRES 1 A 408 GLY PRO ASP GLU GLU PRO GLU GLU PRO GLY ARG ARG GLY SEQRES 2 A 408 SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER SEQRES 3 A 408 GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO SEQRES 4 A 408 PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SER SEQRES 5 A 408 ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS SEQRES 6 A 408 ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP SEQRES 7 A 408 LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS SEQRES 8 A 408 TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO SEQRES 9 A 408 HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA SEQRES 10 A 408 ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN SEQRES 11 A 408 TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA SEQRES 12 A 408 ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU SEQRES 13 A 408 VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN SEQRES 14 A 408 LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL SEQRES 15 A 408 LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE SEQRES 16 A 408 ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR PRO SEQRES 17 A 408 ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG SEQRES 18 A 408 VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS SEQRES 19 A 408 GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR SEQRES 20 A 408 THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA SEQRES 21 A 408 VAL LYS SER ILE LYS ALA ALA SER SER THR GLU LYS PHE SEQRES 22 A 408 PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP SEQRES 23 A 408 GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SEQRES 24 A 408 SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE SEQRES 25 A 408 ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL SEQRES 26 A 408 GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE SEQRES 27 A 408 ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY ALA SEQRES 28 A 408 VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA SEQRES 29 A 408 ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL SEQRES 30 A 408 HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE SEQRES 31 A 408 VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO SEQRES 32 A 408 GLN THR ASP GLU SER HET IOD A 393 1 HET IOD A 394 1 HET EV5 A 395 25 HETNAM IOD IODIDE ION HETNAM EV5 (3S)-3-(2-AMINO-5-CHLORO-1H-BENZIMIDAZOL-1-YL)-N- HETNAM 2 EV5 (CYCLOHEXYLMETHYL)PENTANAMIDE FORMUL 2 IOD 2(I 1-) FORMUL 4 EV5 C19 H27 CL N4 O FORMUL 5 HOH *159(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 TYR A 184 5 5 HELIX 5 5 LYS A 238 SER A 252 1 15 HELIX 6 6 PRO A 276 PHE A 280 5 5 HELIX 7 7 LEU A 301 TYR A 305 1 5 HELIX 8 8 GLY A 334 GLU A 339 1 6 HELIX 9 9 ASP A 378 GLY A 383 5 6 SHEET 1 A 9 ARG A 61 PRO A 70 0 SHEET 2 A 9 LYS A 75 SER A 86 -1 O THR A 82 N ARG A 61 SHEET 3 A 9 TYR A 15 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 VAL A 170 N GLY A 8 SHEET 6 A 9 LEU A 149 LEU A 154 -1 N GLN A 153 O SER A 173 SHEET 7 A 9 PHE A 341 ASP A 346 -1 O PHE A 345 N PHE A 150 SHEET 8 A 9 ARG A 351 VAL A 356 -1 O ALA A 355 N TYR A 342 SHEET 9 A 9 TRP A 189 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 THR A 82 N ARG A 61 SHEET 3 B13 VAL A 95 ASP A 106 -1 O ILE A 99 N GLY A 81 SHEET 4 B13 PHE A 38 GLY A 41 1 N PHE A 38 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 15 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 VAL A 170 N GLY A 8 SHEET 10 B13 LEU A 149 LEU A 154 -1 N GLN A 153 O SER A 173 SHEET 11 B13 PHE A 341 ASP A 346 -1 O PHE A 345 N PHE A 150 SHEET 12 B13 ARG A 351 VAL A 356 -1 O ALA A 355 N TYR A 342 SHEET 13 B13 TRP A 189 PRO A 192 -1 N THR A 191 O ILE A 352 SHEET 1 C 5 GLN A 211 ASP A 212 0 SHEET 2 C 5 ILE A 203 ILE A 208 -1 N ILE A 208 O GLN A 211 SHEET 3 C 5 ILE A 283 MET A 288 -1 O TYR A 286 N ARG A 205 SHEET 4 C 5 GLN A 294 ILE A 300 -1 O PHE A 296 N LEU A 287 SHEET 5 C 5 ALA A 369 VAL A 375 -1 O ALA A 369 N THR A 299 SHEET 1 D 4 SER A 225 VAL A 227 0 SHEET 2 D 4 THR A 331 MET A 333 1 O MET A 333 N ILE A 226 SHEET 3 D 4 LEU A 234 PRO A 237 -1 N ARG A 235 O VAL A 332 SHEET 4 D 4 ILE A 324 SER A 327 1 O SER A 327 N LEU A 236 SHEET 1 E 2 LEU A 306 PRO A 308 0 SHEET 2 E 2 TYR A 320 PHE A 322 -1 O LYS A 321 N ARG A 307 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.03 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.03 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.03 CISPEP 1 SER A 22 PRO A 23 0 1.29 CISPEP 2 ARG A 128 PRO A 129 0 6.89 CISPEP 3 TYR A 222 ASP A 223 0 1.92 CISPEP 4 ALA A 272 GLY A 273 0 2.75 CISPEP 5 THR A 274 THR A 275 0 1.46 CISPEP 6 GLY A 372 PRO A 373 0 -1.20 SITE 1 AC1 2 SER A 105 HOH A 503 SITE 1 AC2 2 HIS A 45 LYS A 107 SITE 1 AC3 9 ASP A 32 GLY A 34 TYR A 71 GLN A 73 SITE 2 AC3 9 TRP A 76 PHE A 108 ASP A 228 GLY A 230 SITE 3 AC3 9 THR A 231 CRYST1 100.190 100.190 172.840 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 0.009981 0.005763 0.000000 0.00000 SCALE2 0.000000 0.011525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005786 0.00000