HEADER HYDROLASE/HYDROLASE INHIBITOR 23-FEB-12 4DV9 TITLE CRYSTAL STRUCTURE OF BACE1 WITH ITS 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: BACE1, 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; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: METHYL (2S)-1-[(2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-AMINO- COMPND 13 3-OXOPROPYL)-2,13-DIBENZYL-12,22-DIHYDROXY-3,5,17-TRIMETHYL-8-(2- COMPND 14 METHYLPROPYL)-4,7,10,15,18,21-HEXAOXO-19-(PROPAN-2-YL)-3,6,9,14,17, COMPND 15 20-HEXAAZATRICOSAN-1-OYL]PYRROLIDINE-2-CARBOXYLATE (NON-PREFERRED COMPND 16 NAME); COMPND 17 CHAIN: B; COMPND 18 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; 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: SYNTHETIC PEPTIDE INHIBITOR KEYWDS HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.XU,W.Y.CHEN,L.LI,T.T.CHEN REVDAT 2 15-SEP-21 4DV9 1 SOURCE REMARK SEQADV LINK REVDAT 1 16-JAN-13 4DV9 0 JRNL AUTH Y.LIU,W.ZHANG,L.LI,L.A.SALVADOR,T.T.CHEN,W.Y.CHEN, JRNL AUTH 2 K.M.FELSENSTEIN,T.B.LADD,A.R.PRICE,T.E.GOLDE,J.HE,Y.C.XU, JRNL AUTH 3 Y.LI,H.LUESCH JRNL TITL CYANOBACTERIAL PEPTIDES AS A PROTOTYPE FOR THE DESIGN OF JRNL TITL 2 POTENT BETA-SECRETASE INHIBITORS AND THE DEVELOPMENT OF JRNL TITL 3 SELECTIVE CHEMICAL PROBES FOR OTHER ASPARTIC PROTEASES JRNL REF J.MED.CHEM. V. 55 10749 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 23181502 JRNL DOI 10.1021/JM301630S REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 30975 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1562 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.3248 - 4.6133 0.98 2836 162 0.1827 0.1997 REMARK 3 2 4.6133 - 3.6629 0.99 2754 156 0.1419 0.1695 REMARK 3 3 3.6629 - 3.2002 0.99 2745 158 0.1657 0.2056 REMARK 3 4 3.2002 - 2.9078 1.00 2777 127 0.1883 0.2349 REMARK 3 5 2.9078 - 2.6995 0.99 2718 146 0.2013 0.2541 REMARK 3 6 2.6995 - 2.5403 0.99 2726 142 0.1831 0.2558 REMARK 3 7 2.5403 - 2.4132 0.98 2685 138 0.1711 0.2164 REMARK 3 8 2.4132 - 2.3081 0.98 2700 135 0.1603 0.2023 REMARK 3 9 2.3081 - 2.2193 0.84 2297 118 0.1514 0.2221 REMARK 3 10 2.2193 - 2.1427 0.98 2640 149 0.1666 0.1825 REMARK 3 11 2.1427 - 2.0757 0.93 2535 131 0.1971 0.2378 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 34.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.78880 REMARK 3 B22 (A**2) : 8.10780 REMARK 3 B33 (A**2) : -2.31900 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3133 REMARK 3 ANGLE : 1.076 4265 REMARK 3 CHIRALITY : 0.077 465 REMARK 3 PLANARITY : 0.004 542 REMARK 3 DIHEDRAL : 14.667 1101 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4DV9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000070825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-12 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97907 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31388 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.076 REMARK 200 RESOLUTION RANGE LOW (A) : 35.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : 0.28100 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7M LI2SO4, 100MM HEPES, 25% PEG3350, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.38300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.38300 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 52.76400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.42300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 52.76400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.42300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.38300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 52.76400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.42300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.38300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 52.76400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.42300 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 400 THE METHYL (2S)-1-[(2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-AMINO-3- REMARK 400 OXOPROPYL)-2,13-DIBENZYL-12,22-DIHYDROXY-3,5,17-TRIMETHYL-8-(2- REMARK 400 METHYLPROPYL)-4,7,10,15,18,21-HEXAOXO-19-(PROPAN-2-YL)-3,6,9,14,17, REMARK 400 20-HEXAAZATRICOSAN-1-OYL]PYRROLIDINE-2-CARBOXYLATE (NON-PREFERRED REMARK 400 NAME) IS POLYPEPTIDE, A MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: METHYL (2S)-1-[(2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-AMINO-3- REMARK 400 OXOPROPYL)-2,13-DIBENZYL-12,22-DIHYDROXY-3,5,17-TRIMETHYL-8- REMARK 400 (2-METHYLPROPYL)-4,7,10,15,18,21-HEXAOXO-19-(PROPAN-2-YL)-3, REMARK 400 6,9,14,17,20-HEXAAZATRICOSAN-1-OYL]PYRROLIDINE-2- REMARK 400 CARBOXYLATE (NON-PREFERRED NAME) REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 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 ALA A 168 REMARK 465 SER A 169 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 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 ARG A -5 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 4 CG OD1 OD2 REMARK 470 ARG A 7 CD NE CZ NH1 NH2 REMARK 470 GLU A 79 CD OE1 OE2 REMARK 470 GLU A 104 CD OE1 OE2 REMARK 470 GLU A 125 CD OE1 OE2 REMARK 470 GLU A 242 CD OE1 OE2 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 GNC B 3 C PSA B 4 N 0.144 REMARK 500 ALA B 6 C ZAE B 7 N 0.161 REMARK 500 ZAE B 7 C PLJ B 8 N 0.162 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 -65.69 -101.35 REMARK 500 ASN A 114 0.15 82.46 REMARK 500 TRP A 197 -82.69 -139.55 REMARK 500 ARG A 205 148.09 -171.31 REMARK 500 ASP A 363 -167.16 -129.26 REMARK 500 ZAE B 7 31.02 -89.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PSA B 4 LEU B 5 -113.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PSA B 4 31.24 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 SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF 8-MER PEPTIDE REMARK 800 INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UQP RELATED DB: PDB REMARK 900 RELATED ID: 3UQR RELATED DB: PDB REMARK 900 RELATED ID: 3UQU RELATED DB: PDB REMARK 900 RELATED ID: 3UQW RELATED DB: PDB REMARK 900 RELATED ID: 3UQX RELATED DB: PDB REMARK 900 RELATED ID: 4DVF RELATED DB: PDB DBREF 4DV9 A -18 393 UNP P56817 BACE1_HUMAN 43 454 DBREF 4DV9 B 1 8 PDB 4DV9 4DV9 1 8 SEQADV 4DV9 MET A -39 UNP P56817 EXPRESSION TAG SEQADV 4DV9 GLY A -38 UNP P56817 EXPRESSION TAG SEQADV 4DV9 SER A -37 UNP P56817 EXPRESSION TAG SEQADV 4DV9 SER A -36 UNP P56817 EXPRESSION TAG SEQADV 4DV9 HIS A -35 UNP P56817 EXPRESSION TAG SEQADV 4DV9 HIS A -34 UNP P56817 EXPRESSION TAG SEQADV 4DV9 HIS A -33 UNP P56817 EXPRESSION TAG SEQADV 4DV9 HIS A -32 UNP P56817 EXPRESSION TAG SEQADV 4DV9 HIS A -31 UNP P56817 EXPRESSION TAG SEQADV 4DV9 HIS A -30 UNP P56817 EXPRESSION TAG SEQADV 4DV9 SER A -29 UNP P56817 EXPRESSION TAG SEQADV 4DV9 ALA A -28 UNP P56817 EXPRESSION TAG SEQADV 4DV9 GLY A -27 UNP P56817 EXPRESSION TAG SEQADV 4DV9 GLU A -26 UNP P56817 EXPRESSION TAG SEQADV 4DV9 ASN A -25 UNP P56817 EXPRESSION TAG SEQADV 4DV9 LEU A -24 UNP P56817 EXPRESSION TAG SEQADV 4DV9 TYR A -23 UNP P56817 EXPRESSION TAG SEQADV 4DV9 PHE A -22 UNP P56817 EXPRESSION TAG SEQADV 4DV9 GLN A -21 UNP P56817 EXPRESSION TAG SEQADV 4DV9 GLY A -20 UNP P56817 EXPRESSION TAG SEQADV 4DV9 THR A -19 UNP P56817 EXPRESSION TAG SEQADV 4DV9 ALA A 75 UNP P56817 LYS 136 ENGINEERED MUTATION SEQADV 4DV9 ALA A 77 UNP P56817 GLU 138 ENGINEERED MUTATION 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 ALA TRP ALA 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 SEQRES 1 B 8 2OP VAL GNC PSA LEU ALA ZAE PLJ MODRES 4DV9 GNC B 3 GLN N~2~-METHYL-L-GLUTAMINE MODRES 4DV9 PSA B 4 PHE MODRES 4DV9 PLJ B 8 PRO METHYL L-PROLINATE HET 2OP B 1 5 HET GNC B 3 10 HET PSA B 4 14 HET ZAE B 7 12 HET PLJ B 8 9 HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HETNAM 2OP (2S)-2-HYDROXYPROPANOIC ACID HETNAM GNC N~2~-METHYL-L-GLUTAMINE HETNAM PSA 3-HYDROXY-4-AMINO-5-PHENYLPENTANOIC ACID HETNAM ZAE N-METHYL-D-PHENYLALANINE HETNAM PLJ METHYL L-PROLINATE HETNAM SO4 SULFATE ION FORMUL 2 2OP C3 H6 O3 FORMUL 2 GNC C6 H12 N2 O3 FORMUL 2 PSA C11 H15 N O3 FORMUL 2 ZAE C10 H13 N O2 FORMUL 2 PLJ C6 H11 N O2 FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 HOH *243(H2 O) HELIX 1 1 PHE A -1 VAL A 3 5 5 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 ASN A 221 1 6 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 GLY A 334 GLU A 339 1 6 HELIX 12 12 ARG A 347 ARG A 349 5 3 HELIX 13 13 ASP A 378 GLY A 383 5 6 SHEET 1 A 9 ARG A 61 PRO A 70 0 SHEET 2 A 9 ALA 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 GLY A 8 -1 N ARG A 7 O TYR A 15 SHEET 5 A 9 GLY A 171 ILE A 176 -1 O GLY A 172 N LEU A 6 SHEET 6 A 9 PHE A 150 CYS A 155 -1 N CYS A 155 O GLY A 171 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 ALA A 75 SER A 86 -1 O LEU A 80 N LYS A 65 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 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 TYR A 14 VAL A 20 -1 N TYR A 14 O VAL A 31 SHEET 8 B13 LEU A 6 GLY A 8 -1 N ARG A 7 O TYR A 15 SHEET 9 B13 GLY A 171 ILE A 176 -1 O GLY A 172 N LEU A 6 SHEET 10 B13 PHE A 150 CYS A 155 -1 N CYS A 155 O GLY A 171 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 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 ILE A 300 N ILE A 283 SHEET 5 C 5 ALA A 369 VAL A 375 -1 O GLU A 371 N ARG A 297 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 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 2.04 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.05 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.03 LINK C 2OP B 1 N VAL B 2 1555 1555 1.45 LINK C VAL B 2 N GNC B 3 1555 1555 1.47 LINK C GNC B 3 N PSA B 4 1555 1555 1.48 LINK C PSA B 4 N LEU B 5 1555 1555 1.47 LINK C ALA B 6 N ZAE B 7 1555 1555 1.50 LINK C ZAE B 7 N PLJ B 8 1555 1555 1.50 CISPEP 1 SER A 22 PRO A 23 0 -4.08 CISPEP 2 ARG A 128 PRO A 129 0 3.60 CISPEP 3 TYR A 222 ASP A 223 0 4.68 CISPEP 4 GLU A 310 ASP A 311 0 -0.20 CISPEP 5 GLY A 372 PRO A 373 0 -0.79 SITE 1 AC1 3 ARG A 50 TYR A 51 GLN A 53 SITE 1 AC2 5 TYR A 51 GLN A 53 GLN A 55 LYS A 218 SITE 2 AC2 5 HOH A 725 SITE 1 AC3 5 ARG A 96 GLU A 134 SER A 139 GLN A 143 SITE 2 AC3 5 HOH A 679 SITE 1 AC4 6 SER A 22 PRO A 23 SER A 58 HIS A 145 SITE 2 AC4 6 PRO A 147 HOH A 554 SITE 1 AC5 26 GLY A 11 LEU A 30 ASP A 32 GLY A 34 SITE 2 AC5 26 VAL A 69 PRO A 70 TYR A 71 THR A 72 SITE 3 AC5 26 GLN A 73 PHE A 108 ILE A 110 ILE A 126 SITE 4 AC5 26 LEU A 188 TYR A 190 TRP A 197 TYR A 198 SITE 5 AC5 26 ASP A 228 GLY A 230 THR A 231 THR A 232 SITE 6 AC5 26 ARG A 235 HOH A 547 HOH A 581 HOH A 593 SITE 7 AC5 26 HOH A 680 HOH B 101 CRYST1 105.528 128.846 76.766 90.00 90.00 90.00 C 2 2 21 8 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 0.009476 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007761 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013027 0.00000