HEADER HYDROLASE/HYDROLASE INHIBITOR 05-JUN-18 6DMI TITLE A MULTICONFORMER LIGAND MODEL OF 5T5 BOUND TO BACE-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASPARTYL PROTEASE 2,ASP 2,BETA-SITE AMYLOID PRECURSOR COMPND 5 PROTEIN CLEAVING ENZYME 1,BETA-SITE APP CLEAVING ENZYME 1,MEMAPSIN-2, COMPND 6 MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; COMPND 7 EC: 3.4.23.46; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BACE1, BACE, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, MULTICONFORMER MODEL, HYDROLASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.M.HUDSON,G.VAN ZUNDERT,D.A.KEEDY,R.FONSECA,A.HELIOU,P.SURESH, AUTHOR 2 K.BORRELLI,T.DAY,J.S.FRASER,H.VAN DEN BEDEM REVDAT 3 01-MAY-24 6DMI 1 AUTHOR LINK REVDAT 2 24-APR-19 6DMI 1 JRNL REVDAT 1 19-DEC-18 6DMI 0 JRNL AUTH G.C.P.VAN ZUNDERT,B.M.HUDSON,S.H.P.DE OLIVEIRA,D.A.KEEDY, JRNL AUTH 2 R.FONSECA,A.HELIOU,P.SURESH,K.BORRELLI,T.DAY,J.S.FRASER, JRNL AUTH 3 H.VAN DEN BEDEM JRNL TITL QFIT-LIGAND REVEALS WIDESPREAD CONFORMATIONAL HETEROGENEITY JRNL TITL 2 OF DRUG-LIKE MOLECULES IN X-RAY ELECTRON DENSITY MAPS. JRNL REF J. MED. CHEM. V. 61 11183 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30457858 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01292 REMARK 0 REMARK 0 THIS ENTRY 6DMI REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 DATA IN 5EZX, DETERMINED BY .KUHN,W.GUBA,J.HERT,D.BANNER, REMARK 0 C.BISSANTZ,S.CECCARELLI,W.HAAP,M.KORNER,A.KUGLSTATTER,C.LERNER, REMARK 0 P.MATTEI,W.NEIDHART,E.PINARD,M.G.RUDOLPH,T.SCHULZ-GASCH, REMARK 0 T.WOLTERING,M.STAHL REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.KUHN,W.GUBA,J.HERT,D.BANNER,C.BISSANTZ,S.CECCARELLI, REMARK 1 AUTH 2 W.HAAP,M.KORNER,A.KUGLSTATTER,C.LERNER,P.MATTEI,W.NEIDHART, REMARK 1 AUTH 3 E.PINARD,M.G.RUDOLPH,T.SCHULZ-GASCH,T.WOLTERING,M.STAHL REMARK 1 TITL A REAL-WORLD PERSPECTIVE ON MOLECULAR DESIGN. REMARK 1 REF J. MED. CHEM. V. 59 4087 2016 REMARK 1 REFN ISSN 1520-4804 REMARK 1 PMID 26878596 REMARK 1 DOI 10.1021/ACS.JMEDCHEM.5B01875 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11_2558 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 41604 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 47.7188 - 4.5781 0.98 3062 154 0.1815 0.1819 REMARK 3 2 4.5781 - 3.6342 1.00 2937 149 0.1536 0.1871 REMARK 3 3 3.6342 - 3.1749 1.00 2891 146 0.1748 0.1994 REMARK 3 4 3.1749 - 2.8847 1.00 2857 144 0.1908 0.2304 REMARK 3 5 2.8847 - 2.6779 0.99 2835 144 0.2038 0.2612 REMARK 3 6 2.6779 - 2.5200 0.99 2832 143 0.2002 0.2605 REMARK 3 7 2.5200 - 2.3938 0.99 2806 141 0.2064 0.2648 REMARK 3 8 2.3938 - 2.2896 0.99 2807 142 0.2059 0.2867 REMARK 3 9 2.2896 - 2.2015 0.99 2771 140 0.2131 0.2202 REMARK 3 10 2.2015 - 2.1255 0.99 2784 141 0.2165 0.2832 REMARK 3 11 2.1255 - 2.0591 0.99 2755 138 0.2287 0.2511 REMARK 3 12 2.0591 - 2.0002 0.99 2770 140 0.2439 0.3124 REMARK 3 13 2.0002 - 1.9476 0.98 2743 139 0.2587 0.2868 REMARK 3 14 1.9476 - 1.9000 0.98 2754 139 0.2878 0.3163 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.10 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.014 3185 REMARK 3 ANGLE : 1.171 4334 REMARK 3 CHIRALITY : 0.070 461 REMARK 3 PLANARITY : 0.007 558 REMARK 3 DIHEDRAL : 6.762 3136 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 6DMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.330 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 5EZX REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5M SODIUM FORMATE, 100MM HEPES, 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 56.60667 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 113.21333 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 84.91000 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 141.51667 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 28.30333 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 56.60667 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 113.21333 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 141.51667 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 84.91000 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 28.30333 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 219 REMARK 465 PHE A 220 REMARK 465 PRO A 221 REMARK 465 LEU A 222 REMARK 465 ASN A 223 REMARK 465 GLN A 224 REMARK 465 SER A 225 REMARK 465 GLU A 226 REMARK 465 VAL A 227 REMARK 465 LEU A 228 REMARK 465 ALA A 229 REMARK 465 GLU A 371 REMARK 465 ASP A 372 REMARK 465 VAL A 373 REMARK 465 ALA A 374 REMARK 465 THR A 375 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 OE2 GLU A 425 O HOH A 601 1.96 REMARK 500 O HOH A 663 O HOH A 782 1.96 REMARK 500 O HOH A 843 O HOH A 877 1.96 REMARK 500 O HOH A 806 O HOH A 834 2.03 REMARK 500 O HOH A 892 O HOH A 924 2.04 REMARK 500 O HOH A 682 O HOH A 902 2.09 REMARK 500 O HOH A 797 O HOH A 887 2.14 REMARK 500 O HOH A 713 O HOH A 929 2.15 REMARK 500 O HOH A 825 O HOH A 913 2.16 REMARK 500 O HOH A 680 O HOH A 844 2.16 REMARK 500 O HOH A 706 O HOH A 748 2.18 REMARK 500 O HIS A 421 O HOH A 602 2.18 REMARK 500 O LEU A 367 O HOH A 604 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 883 O HOH A 883 10665 2.04 REMARK 500 O HOH A 890 O HOH A 890 12566 2.11 REMARK 500 O HOH A 794 O HOH A 883 10665 2.14 REMARK 500 O HOH A 640 O HOH A 899 6555 2.16 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 132 -158.30 -160.46 REMARK 500 LYS A 136 148.48 -170.05 REMARK 500 HIS A 150 45.98 -101.84 REMARK 500 PHE A 169 -62.54 -101.22 REMARK 500 TRP A 258 -84.37 -139.97 REMARK 500 HIS A 423 -152.36 -140.96 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 TRP A 258 TYR A 259 149.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 202 O REMARK 620 2 THR A 205 O 82.7 REMARK 620 3 HOH A 694 O 95.6 95.7 REMARK 620 4 HOH A 754 O 100.9 73.2 158.7 REMARK 620 5 HOH A 875 O 95.4 169.7 94.5 97.3 REMARK 620 6 HOH A 886 O 169.6 88.1 90.3 71.5 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 242 O REMARK 620 2 TYR A 245 O 83.6 REMARK 620 3 HOH A 699 O 157.6 102.0 REMARK 620 4 HOH A 720 O 84.9 72.4 117.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5T5 A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EZX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH {(1R,2R)-2-[(R)-2-AMINO- REMARK 900 4-(4-DIFLUOROMETHOXY-PHENYL)-4,5-DIHYDRO-OXAZOL-4-YL]-CYCLOPROPYL}- REMARK 900 (5-CHLORO-PYRIDIN-3-YL)-METHANONE DBREF 6DMI A 57 446 UNP P56817 BACE1_HUMAN 57 446 SEQADV 6DMI ALA A 307 UNP P56817 LYS 307 CONFLICT SEQRES 1 A 390 ARG GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY SEQRES 2 A 390 LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SEQRES 3 A 390 SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SEQRES 4 A 390 SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE SEQRES 5 A 390 LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR SEQRES 6 A 390 ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN SEQRES 7 A 390 GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER SEQRES 8 A 390 ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE SEQRES 9 A 390 ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SEQRES 10 A 390 SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU SEQRES 11 A 390 ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SEQRES 12 A 390 SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER SEQRES 13 A 390 LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER SEQRES 14 A 390 GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY SEQRES 15 A 390 GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR SEQRES 16 A 390 THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE SEQRES 17 A 390 VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP SEQRES 18 A 390 CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER SEQRES 19 A 390 GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU SEQRES 20 A 390 ALA ALA VAL ALA SER ILE LYS ALA ALA SER SER THR GLU SEQRES 21 A 390 LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL SEQRES 22 A 390 CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO SEQRES 23 A 390 VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SEQRES 24 A 390 SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG SEQRES 25 A 390 PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR SEQRES 26 A 390 LYS PHE ALA ILE SER GLN SER SER THR GLY THR VAL MET SEQRES 27 A 390 GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP SEQRES 28 A 390 ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS SEQRES 29 A 390 HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY SEQRES 30 A 390 PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN HET NA A 501 1 HET DMS A 502 4 HET NA A 503 1 HET 5T5 A 504 84 HETNAM NA SODIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM 5T5 [(1~{R},2~{R})-2-[(4~{S})-2-AZANYL-4-[4- HETNAM 2 5T5 [BIS(FLUORANYL)METHOXY]PHENYL]-5~{H}-1,3-OXAZOL-4- HETNAM 3 5T5 YL]CYCLOPROPYL]-(5-CHLORANYLPYRIDIN-3-YL)METHANONE FORMUL 2 NA 2(NA 1+) FORMUL 3 DMS C2 H6 O S FORMUL 5 5T5 C19 H16 CL F2 N3 O3 FORMUL 6 HOH *340(H2 O) HELIX 1 AA1 PHE A 60 VAL A 64 5 5 HELIX 2 AA2 GLN A 114 SER A 118 5 5 HELIX 3 AA3 TYR A 184 ALA A 188 5 5 HELIX 4 AA4 PRO A 196 THR A 205 1 10 HELIX 5 AA5 ASP A 241 SER A 243 5 3 HELIX 6 AA6 ASP A 277 TYR A 283 5 7 HELIX 7 AA7 LYS A 299 SER A 313 1 15 HELIX 8 AA8 PRO A 319 LEU A 324 1 6 HELIX 9 AA9 LEU A 362 TYR A 366 1 5 HELIX 10 AB1 GLY A 395 GLU A 400 1 6 HELIX 11 AB2 ARG A 408 ARG A 410 5 3 HELIX 12 AB3 ASP A 439 GLY A 444 5 6 SHEET 1 AA1 9 ARG A 122 TYR A 132 0 SHEET 2 AA1 9 GLY A 135 SER A 147 -1 O GLY A 139 N VAL A 128 SHEET 3 AA1 9 TYR A 75 VAL A 81 -1 N THR A 80 O SER A 147 SHEET 4 AA1 9 LEU A 67 GLY A 69 -1 N ARG A 68 O TYR A 76 SHEET 5 AA1 9 VAL A 231 ILE A 237 -1 O GLY A 233 N LEU A 67 SHEET 6 AA1 9 PHE A 211 CYS A 216 -1 N CYS A 216 O GLY A 232 SHEET 7 AA1 9 PHE A 402 ASP A 407 -1 O PHE A 406 N PHE A 211 SHEET 8 AA1 9 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403 SHEET 9 AA1 9 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413 SHEET 1 AA213 ARG A 122 TYR A 132 0 SHEET 2 AA213 GLY A 135 SER A 147 -1 O GLY A 139 N VAL A 128 SHEET 3 AA213 VAL A 156 ASP A 167 -1 O VAL A 156 N VAL A 146 SHEET 4 AA213 PHE A 99 GLY A 102 1 N VAL A 101 O ILE A 163 SHEET 5 AA213 GLY A 178 GLY A 181 -1 O ILE A 179 N ALA A 100 SHEET 6 AA213 GLN A 86 ASP A 93 1 N LEU A 91 O LEU A 180 SHEET 7 AA213 TYR A 75 VAL A 81 -1 N TYR A 75 O VAL A 92 SHEET 8 AA213 LEU A 67 GLY A 69 -1 N ARG A 68 O TYR A 76 SHEET 9 AA213 VAL A 231 ILE A 237 -1 O GLY A 233 N LEU A 67 SHEET 10 AA213 PHE A 211 CYS A 216 -1 N CYS A 216 O GLY A 232 SHEET 11 AA213 PHE A 402 ASP A 407 -1 O PHE A 406 N PHE A 211 SHEET 12 AA213 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403 SHEET 13 AA213 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413 SHEET 1 AA3 5 GLN A 272 ASP A 273 0 SHEET 2 AA3 5 ILE A 264 ILE A 269 -1 N ILE A 269 O GLN A 272 SHEET 3 AA3 5 ILE A 344 MET A 349 -1 O TYR A 347 N ARG A 266 SHEET 4 AA3 5 GLN A 355 ILE A 361 -1 O ILE A 361 N ILE A 344 SHEET 5 AA3 5 ALA A 430 VAL A 436 -1 O GLU A 432 N ARG A 358 SHEET 1 AA4 4 SER A 286 VAL A 288 0 SHEET 2 AA4 4 THR A 392 MET A 394 1 O MET A 394 N ILE A 287 SHEET 3 AA4 4 LEU A 295 PRO A 298 -1 N ARG A 296 O VAL A 393 SHEET 4 AA4 4 ILE A 385 SER A 388 1 O SER A 386 N LEU A 297 SHEET 1 AA5 3 VAL A 329 TRP A 331 0 SHEET 2 AA5 3 ASP A 379 PHE A 383 -1 O ASP A 379 N TRP A 331 SHEET 3 AA5 3 LEU A 367 PRO A 369 -1 N ARG A 368 O LYS A 382 SSBOND 1 CYS A 216 CYS A 420 1555 1555 2.10 SSBOND 2 CYS A 278 CYS A 443 1555 1555 2.06 SSBOND 3 CYS A 330 CYS A 380 1555 1555 2.04 LINK O VAL A 202 NA NA A 503 1555 1555 2.34 LINK O THR A 205 NA NA A 503 1555 1555 2.39 LINK O HIS A 242 NA NA A 501 1555 1555 2.50 LINK O TYR A 245 NA NA A 501 1555 1555 2.25 LINK NA NA A 501 O HOH A 699 1555 1555 2.32 LINK NA NA A 501 O HOH A 720 1555 1555 2.37 LINK NA NA A 503 O HOH A 694 1555 1555 2.31 LINK NA NA A 503 O HOH A 754 1555 1555 2.31 LINK NA NA A 503 O HOH A 875 1555 1555 2.03 LINK NA NA A 503 O HOH A 886 1555 1555 2.52 CISPEP 1 SER A 83 PRO A 84 0 -0.70 CISPEP 2 THR A 133 GLN A 134 0 -6.36 CISPEP 3 ARG A 189 PRO A 190 0 4.76 CISPEP 4 TYR A 283 ASP A 284 0 2.60 CISPEP 5 GLY A 433 PRO A 434 0 -6.71 SITE 1 AC1 4 HIS A 242 TYR A 245 HOH A 699 HOH A 720 SITE 1 AC2 3 ARG A 157 ASN A 159 GLU A 195 SITE 1 AC3 6 VAL A 202 THR A 205 HOH A 694 HOH A 754 SITE 2 AC3 6 HOH A 875 HOH A 886 SITE 1 AC4 27 GLY A 72 GLN A 73 GLY A 74 LEU A 91 SITE 2 AC4 27 ASP A 93 GLY A 95 SER A 96 ASN A 98 SITE 3 AC4 27 VAL A 130 TYR A 132 TRP A 137 ILE A 171 SITE 4 AC4 27 TRP A 176 ILE A 179 ARG A 189 ASP A 289 SITE 5 AC4 27 SER A 290 GLY A 291 THR A 292 THR A 293 SITE 6 AC4 27 HOH A 650 HOH A 670 HOH A 675 HOH A 687 SITE 7 AC4 27 HOH A 768 HOH A 769 HOH A 842 CRYST1 102.320 102.320 169.820 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 0.009773 0.005643 0.000000 0.00000 SCALE2 0.000000 0.011285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005889 0.00000