PDB Short entry for 4J5D HEADER ISOMERASE/ISOMERASE INHIBITOR COMPLEX 08-FEB-13 4J5D TITLE HUMAN CYCLOPHILIN D COMPLEXED WITH AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: UNP RESIDUES 44-207; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CYP3, PPIF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE-ISOMERASE INHIBITOR COMPLEX COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.GELIN,L.COLLIANDRE,Y.BESSIN,J.F.GUICHOU REVDAT 3 28-FEB-24 4J5D 1 REMARK SEQADV REVDAT 2 19-OCT-16 4J5D 1 JRNL REVDAT 1 19-FEB-14 4J5D 0 JRNL AUTH A.AHMED-BELKACEM,L.COLLIANDRE,N.AHNOU,Q.NEVERS,M.GELIN, JRNL AUTH 2 Y.BESSIN,R.BRILLET,O.CALA,D.DOUGUET,W.BOURGUET,I.KRIMM, JRNL AUTH 3 J.M.PAWLOTSKY,J.F.GUICHOU JRNL TITL FRAGMENT-BASED DISCOVERY OF A NEW FAMILY OF NON-PEPTIDIC JRNL TITL 2 SMALL-MOLECULE CYCLOPHILIN INHIBITORS WITH POTENT ANTIVIRAL JRNL TITL 3 ACTIVITIES. JRNL REF NAT COMMUN V. 7 12777 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27652979 JRNL DOI 10.1038/NCOMMS12777 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 32346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1546 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 28.2950 - 3.6395 1.00 2888 147 0.1184 0.1594 REMARK 3 2 3.6395 - 2.8897 1.00 2872 146 0.0933 0.1068 REMARK 3 3 2.8897 - 2.5247 1.00 2870 158 0.1067 0.1409 REMARK 3 4 2.5247 - 2.2940 1.00 2897 124 0.0974 0.1129 REMARK 3 5 2.2940 - 2.1296 1.00 2903 134 0.0840 0.1701 REMARK 3 6 2.1296 - 2.0041 1.00 2868 170 0.0849 0.1226 REMARK 3 7 2.0041 - 1.9037 1.00 2868 154 0.0870 0.1664 REMARK 3 8 1.9037 - 1.8209 1.00 2874 150 0.0930 0.1277 REMARK 3 9 1.8209 - 1.7508 1.00 2893 155 0.0976 0.1484 REMARK 3 10 1.7508 - 1.6904 1.00 2853 173 0.1065 0.1440 REMARK 3 11 1.6904 - 1.6375 1.00 2856 160 0.1121 0.1393 REMARK 3 12 1.6375 - 1.5907 1.00 2922 135 0.1218 0.1805 REMARK 3 13 1.5907 - 1.5489 1.00 2860 148 0.1292 0.1805 REMARK 3 14 1.5489 - 1.5111 0.99 2785 183 0.1521 0.2004 REMARK 3 15 1.5111 - 1.4767 0.96 2765 148 0.1809 0.2153 REMARK 3 16 1.4767 - 1.4453 0.92 2658 133 0.2108 0.2236 REMARK 3 17 1.4453 - 1.4164 0.85 2466 106 0.2330 0.2617 REMARK 3 18 1.4164 - 1.3897 0.78 2184 149 0.2581 0.2998 REMARK 3 19 1.3897 - 1.3649 0.68 1977 118 0.2871 0.3506 REMARK 3 20 1.3649 - 1.3417 0.58 1684 90 0.3024 0.3058 REMARK 3 21 1.3417 - 1.3200 0.49 1413 54 0.3095 0.3239 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.95 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 : 0.009 1360 REMARK 3 ANGLE : 1.277 1832 REMARK 3 CHIRALITY : 0.088 200 REMARK 3 PLANARITY : 0.005 233 REMARK 3 DIHEDRAL : 12.702 515 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 4J5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93340 REMARK 200 MONOCHROMATOR : ASYMMETRIC LAUE 001 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.19 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32346 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 28.296 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : 0.49300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, PH 7.3, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 43.61000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.29500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.80500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.29500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.41500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.29500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.29500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.80500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.29500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.29500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.41500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.61000 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: X 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 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 X 102 -83.82 -143.00 REMARK 500 ASN X 113 -1.23 -146.00 REMARK 500 THR X 161 64.21 -105.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH X 702 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 728 X 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J58 RELATED DB: PDB REMARK 900 RELATED ID: 4J59 RELATED DB: PDB REMARK 900 RELATED ID: 4J5A RELATED DB: PDB REMARK 900 RELATED ID: 4J5B RELATED DB: PDB REMARK 900 RELATED ID: 4J5C RELATED DB: PDB REMARK 900 RELATED ID: 4J5E RELATED DB: PDB DBREF 4J5D X 44 207 UNP P30405 PPIF_HUMAN 44 207 SEQADV 4J5D ILE X 175 UNP P30405 LYS 175 ENGINEERED MUTATION SEQRES 1 X 164 GLY ASN PRO LEU VAL TYR LEU ASP VAL ASP ALA ASN GLY SEQRES 2 X 164 LYS PRO LEU GLY ARG VAL VAL LEU GLU LEU LYS ALA ASP SEQRES 3 X 164 VAL VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU CYS SEQRES 4 X 164 THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER THR PHE SEQRES 5 X 164 HIS ARG VAL ILE PRO SER PHE MET CYS GLN ALA GLY ASP SEQRES 6 X 164 PHE THR ASN HIS ASN GLY THR GLY GLY LYS SER ILE TYR SEQRES 7 X 164 GLY SER ARG PHE PRO ASP GLU ASN PHE THR LEU LYS HIS SEQRES 8 X 164 VAL GLY PRO GLY VAL LEU SER MET ALA ASN ALA GLY PRO SEQRES 9 X 164 ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ILE LYS SEQRES 10 X 164 THR ASP TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY HIS SEQRES 11 X 164 VAL ILE GLU GLY MET ASP VAL VAL LYS LYS ILE GLU SER SEQRES 12 X 164 PHE GLY SER LYS SER GLY ARG THR SER LYS LYS ILE VAL SEQRES 13 X 164 ILE THR ASP CYS GLY GLN LEU SER HET 728 X 301 27 HETNAM 728 1-(4-AMINOBENZYL)-3-{2-[(2R)-2-(2-BROMOPHENYL) HETNAM 2 728 PYRROLIDIN-1-YL]-2-OXOETHYL}UREA FORMUL 2 728 C20 H23 BR N4 O2 FORMUL 3 HOH *347(H2 O) HELIX 1 1 VAL X 71 GLY X 84 1 14 HELIX 2 2 THR X 161 ASP X 165 5 5 HELIX 3 3 GLY X 177 PHE X 187 1 11 SHEET 1 A 8 PHE X 95 ILE X 99 0 SHEET 2 A 8 MET X 103 ALA X 106 -1 O GLN X 105 N ARG X 97 SHEET 3 A 8 PHE X 154 CYS X 157 -1 O PHE X 154 N ALA X 106 SHEET 4 A 8 VAL X 139 MET X 142 -1 N VAL X 139 O CYS X 157 SHEET 5 A 8 VAL X 170 GLU X 176 -1 O GLY X 172 N LEU X 140 SHEET 6 A 8 LYS X 57 LEU X 66 -1 N VAL X 63 O ILE X 175 SHEET 7 A 8 LEU X 47 ALA X 54 -1 N VAL X 52 O LEU X 59 SHEET 8 A 8 ILE X 198 GLN X 205 -1 O ASP X 202 N ASP X 51 SITE 1 AC1 14 ARG X 97 MET X 103 GLN X 105 GLY X 114 SITE 2 AC1 14 ARG X 124 ALA X 143 ASN X 144 THR X 149 SITE 3 AC1 14 GLN X 153 PHE X 155 LEU X 164 HIS X 168 SITE 4 AC1 14 HOH X 466 HOH X 548 CRYST1 56.590 56.590 87.220 90.00 90.00 90.00 P 41 21 2 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 0.017671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011465 0.00000