PDB Short entry for 3TPR HEADER HYDROLASE/HYDROLASE INHIBITOR 08-SEP-11 3TPR TITLE CRYSTAL STRUCTURE OF BACE1 COMPLEXED WITH AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 43-454; 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: 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: PET28A KEYWDS MEMAPSIN 2, PROTEASE, BETA-SECRETASE 1, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.XU,M.J.LI,H.GREENBLATT,T.T.CHEN,I.SILMAN,J.L.SUSSMAN REVDAT 4 01-NOV-23 3TPR 1 REMARK SEQADV REVDAT 3 08-NOV-17 3TPR 1 REMARK REVDAT 2 13-JUN-12 3TPR 1 JRNL REVDAT 1 23-NOV-11 3TPR 0 JRNL AUTH Y.C.XU,M.J.LI,H.GREENBLATT,W.Y.CHEN,A.PAZ,O.DYM,Y.PELEG, JRNL AUTH 2 T.T.CHEN,X.SHEN,J.H.HE,H.L.JIANG,I.SILMAN,J.L.SUSSMAN JRNL TITL FLEXIBILITY OF THE FLAP IN THE ACTIVE SITE OF BACE1 AS JRNL TITL 2 REVEALED BY CRYSTAL STRUCTURES AND MOLECULAR DYNAMICS JRNL TITL 3 SIMULATIONS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 13 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 22194329 JRNL DOI 10.1107/S0907444911047251 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 18253 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) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 937 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1253 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2788 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.01000 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): 0.292 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.192 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.604 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2914 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3979 ; 2.023 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 7.831 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;33.989 ;23.361 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 412 ;18.976 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.722 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2257 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1830 ; 1.139 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2934 ; 2.090 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1084 ; 2.755 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1041 ; 4.321 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3TPR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067769. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9395 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18527 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.710 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2B8L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% (W/V) PEG 5000, MONOMETHYL REMARK 280 ETHER, 200MM AMMONIUM IODIDE, 200MM SODIUM CITRATE, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 56.54900 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 113.09800 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 84.82350 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 141.37250 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 28.27450 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 56.54900 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 113.09800 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 141.37250 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 84.82350 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 28.27450 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 433 LIES ON A SPECIAL POSITION. 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 -39 REMARK 465 GLY A -38 REMARK 465 SER A -37 REMARK 465 SER A -36 REMARK 465 HIS A -35 REMARK 465 HIS A -34 REMARK 465 HIS A -33 REMARK 465 HIS A -32 REMARK 465 HIS A -31 REMARK 465 HIS A -30 REMARK 465 SER A -29 REMARK 465 ALA A -28 REMARK 465 GLY A -27 REMARK 465 GLU A -26 REMARK 465 ASN A -25 REMARK 465 LEU A -24 REMARK 465 TYR A -23 REMARK 465 PHE A -22 REMARK 465 GLN A -21 REMARK 465 GLY A -20 REMARK 465 THR A -19 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 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 GLU A 310 REMARK 465 ASP A 311 REMARK 465 VAL A 312 REMARK 465 ALA A 313 REMARK 465 THR A 314 REMARK 465 SER A 315 REMARK 465 GLN A 316 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 465 THR A 393 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 VAL A 0 CG1 CG2 REMARK 470 GLU A 1 CG CD OE1 OE2 REMARK 470 ARG A 7 NE CZ NH1 NH2 REMARK 470 LYS A 9 CE NZ REMARK 470 ARG A 50 NH1 REMARK 470 ARG A 64 NE CZ NH1 NH2 REMARK 470 LYS A 65 CG CD CE NZ REMARK 470 GLN A 73 CG CD OE1 NE2 REMARK 470 LYS A 75 CE NZ REMARK 470 LYS A 107 NZ REMARK 470 GLU A 125 OE1 OE2 REMARK 470 LYS A 142 CE NZ REMARK 470 ALA A 157 CA C O CB REMARK 470 ALA A 168 N CA CB REMARK 470 ILE A 176 CD1 REMARK 470 GLN A 211 CG CD OE1 NE2 REMARK 470 LEU A 213 CD1 CD2 REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 LYS A 218 CD CE NZ REMARK 470 GLU A 219 CG CD OE1 OE2 REMARK 470 LYS A 238 CE NZ REMARK 470 GLU A 242 CD OE1 OE2 REMARK 470 VAL A 245 CG1 CG2 REMARK 470 LYS A 246 CD CE NZ REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 LYS A 256 CG CD CE NZ REMARK 470 PHE A 257 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 259 CG OD1 OD2 REMARK 470 LEU A 263 CG CD1 CD2 REMARK 470 GLU A 265 CG CD OE1 OE2 REMARK 470 GLN A 266 CG CD OE1 NE2 REMARK 470 TRP A 270 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 270 CZ3 CH2 REMARK 470 GLN A 271 CG CD OE1 NE2 REMARK 470 THR A 274 OG1 CG2 REMARK 470 ILE A 279 CG1 CG2 CD1 REMARK 470 LYS A 321 CE NZ REMARK 470 SER A 327 OG REMARK 470 SER A 328 OG REMARK 470 PHE A 365 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 380 CG CD OE1 OE2 REMARK 470 ILE A 386 CA C O CB CG1 CG2 CD1 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 104 CG GLU A 104 CD 0.102 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 -68.02 -104.28 REMARK 500 TRP A 197 -80.67 -135.17 REMARK 500 LYS A 214 44.58 36.66 REMARK 500 PRO A 258 147.00 -39.49 REMARK 500 TRP A 262 50.01 -69.97 REMARK 500 LEU A 263 -156.24 -160.04 REMARK 500 THR A 275 112.48 -37.79 REMARK 500 ILE A 279 1.07 -54.84 REMARK 500 ASP A 346 77.27 -103.16 REMARK 500 ASP A 363 -176.60 -63.97 REMARK 500 ASP A 381 -8.99 -49.35 REMARK 500 ASN A 385 -54.07 -131.83 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 5HA A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 394 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TPJ RELATED DB: PDB REMARK 900 RELATED ID: 3TPL RELATED DB: PDB REMARK 900 RELATED ID: 3TPP RELATED DB: PDB DBREF 3TPR A -18 393 UNP P56817 BACE1_HUMAN 43 454 SEQADV 3TPR MET A -39 UNP P56817 EXPRESSION TAG SEQADV 3TPR GLY A -38 UNP P56817 EXPRESSION TAG SEQADV 3TPR SER A -37 UNP P56817 EXPRESSION TAG SEQADV 3TPR SER A -36 UNP P56817 EXPRESSION TAG SEQADV 3TPR HIS A -35 UNP P56817 EXPRESSION TAG SEQADV 3TPR HIS A -34 UNP P56817 EXPRESSION TAG SEQADV 3TPR HIS A -33 UNP P56817 EXPRESSION TAG SEQADV 3TPR HIS A -32 UNP P56817 EXPRESSION TAG SEQADV 3TPR HIS A -31 UNP P56817 EXPRESSION TAG SEQADV 3TPR HIS A -30 UNP P56817 EXPRESSION TAG SEQADV 3TPR SER A -29 UNP P56817 EXPRESSION TAG SEQADV 3TPR ALA A -28 UNP P56817 EXPRESSION TAG SEQADV 3TPR GLY A -27 UNP P56817 EXPRESSION TAG SEQADV 3TPR GLU A -26 UNP P56817 EXPRESSION TAG SEQADV 3TPR ASN A -25 UNP P56817 EXPRESSION TAG SEQADV 3TPR LEU A -24 UNP P56817 EXPRESSION TAG SEQADV 3TPR TYR A -23 UNP P56817 EXPRESSION TAG SEQADV 3TPR PHE A -22 UNP P56817 EXPRESSION TAG SEQADV 3TPR GLN A -21 UNP P56817 EXPRESSION TAG SEQADV 3TPR GLY A -20 UNP P56817 EXPRESSION TAG SEQADV 3TPR THR A -19 UNP P56817 EXPRESSION TAG SEQRES 1 A 433 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER ALA GLY SEQRES 2 A 433 GLU ASN LEU TYR PHE GLN GLY THR LEU PRO ARG GLU THR SEQRES 3 A 433 ASP GLU GLU PRO GLU GLU PRO GLY ARG ARG GLY SER PHE SEQRES 4 A 433 VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER GLY GLN SEQRES 5 A 433 GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO PRO GLN SEQRES 6 A 433 THR LEU ASN ILE LEU VAL ASP THR GLY SER SER ASN PHE SEQRES 7 A 433 ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS ARG TYR SEQRES 8 A 433 TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP LEU ARG SEQRES 9 A 433 LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS TRP GLU SEQRES 10 A 433 GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO HIS GLY SEQRES 11 A 433 PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA ILE THR SEQRES 12 A 433 GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN TRP GLU SEQRES 13 A 433 GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA ARG PRO SEQRES 14 A 433 ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU VAL LYS SEQRES 15 A 433 GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN LEU CYS SEQRES 16 A 433 GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL LEU ALA SEQRES 17 A 433 SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE ASP HIS SEQRES 18 A 433 SER LEU TYR THR GLY SER LEU TRP TYR THR PRO ILE ARG SEQRES 19 A 433 ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG VAL GLU SEQRES 20 A 433 ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS GLU TYR SEQRES 21 A 433 ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR THR ASN SEQRES 22 A 433 LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA VAL LYS SEQRES 23 A 433 SER ILE LYS ALA ALA SER SER THR GLU LYS PHE PRO ASP SEQRES 24 A 433 GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP GLN ALA SEQRES 25 A 433 GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SER LEU SEQRES 26 A 433 TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE ARG ILE SEQRES 27 A 433 THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL GLU ASP SEQRES 28 A 433 VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE ALA ILE SEQRES 29 A 433 SER GLN SER SER THR GLY THR VAL MET GLY ALA VAL ILE SEQRES 30 A 433 MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA ARG LYS SEQRES 31 A 433 ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL HIS ASP SEQRES 32 A 433 GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE VAL THR SEQRES 33 A 433 LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO GLN THR SEQRES 34 A 433 ASP GLU SER THR HET 5HA A 400 41 HET CL A 394 1 HETNAM 5HA N-[(1S,2R)-1-BENZYL-3-(CYCLOPROPYLAMINO)-2- HETNAM 2 5HA HYDROXYPROPYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'- HETNAM 3 5HA [(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE HETNAM CL CHLORIDE ION FORMUL 2 5HA C31 H38 N4 O5 S FORMUL 3 CL CL 1- FORMUL 4 HOH *85(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 LYS A 218 TYR A 222 5 5 HELIX 6 6 LYS A 238 SER A 252 1 15 HELIX 7 7 PRO A 276 PHE A 280 5 5 HELIX 8 8 LEU A 301 TYR A 305 1 5 HELIX 9 9 GLY A 334 GLU A 339 1 6 HELIX 10 10 MET A 379 GLY A 383 5 5 SHEET 1 A 9 ARG A 61 VAL A 69 0 SHEET 2 A 9 LYS A 75 SER A 86 -1 O TRP A 76 N VAL A 69 SHEET 3 A 9 GLY A 13 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 VAL A 170 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 PHE A 345 N PHE A 150 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 VAL A 69 0 SHEET 2 B13 LYS A 75 SER A 86 -1 O TRP A 76 N VAL A 69 SHEET 3 B13 VAL A 95 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 ILE A 102 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 GLY A 13 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 VAL A 170 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 PHE A 345 N PHE A 150 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 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 PHE A 374 N SER A 295 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 325 N LEU A 236 SHEET 1 E 3 VAL A 268 TRP A 270 0 SHEET 2 E 3 ASP A 318 PHE A 322 -1 O TYR A 320 N VAL A 268 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 2.06 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.09 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.08 CISPEP 1 SER A 22 PRO A 23 0 -1.16 CISPEP 2 ARG A 128 PRO A 129 0 1.47 CISPEP 3 TYR A 222 ASP A 223 0 4.60 CISPEP 4 LEU A 263 GLY A 264 0 13.38 CISPEP 5 GLY A 372 PRO A 373 0 1.58 SITE 1 AC1 13 GLY A 11 GLY A 13 ASP A 32 GLY A 34 SITE 2 AC1 13 SER A 35 TYR A 198 ASP A 228 SER A 229 SITE 3 AC1 13 GLY A 230 THR A 231 THR A 232 ASN A 233 SITE 4 AC1 13 ARG A 235 SITE 1 AC2 1 ARG A 96 CRYST1 104.195 104.195 169.647 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 0.009597 0.005541 0.000000 0.00000 SCALE2 0.000000 0.011082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005895 0.00000