HEADER ISOMERASE/ISOMERASE INHIBITOR 21-MAY-20 6X3R TITLE HUMAN CYCLOPHILIN A BOUND TO A SERIES OF ACYLCIC AND MACROCYCLIC TITLE 2 INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE A,CYCLOPHILIN A,CYCLOSPORIN A-BINDING PROTEIN, COMPND 5 ROTAMASE A; COMPND 6 EC: 5.2.1.8; COMPND 7 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: PPIA, CYPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLOPHILIN A, SANGLIFEHRIN A, PROLYL ISOMERASE, MACROCYLCIC KEYWDS 2 INHIBITOR, PEPTIDOMIMETIC, ISOMERASE-ISOMERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.C.APPLEBY,J.L.PAULSEN,U.SCHMITZ,D.SHIVAKUMAR REVDAT 4 18-OCT-23 6X3R 1 REMARK REVDAT 3 26-AUG-20 6X3R 1 JRNL REVDAT 2 01-JUL-20 6X3R 1 JRNL REVDAT 1 24-JUN-20 6X3R 0 JRNL AUTH J.L.PAULSEN,H.S.YU,D.SINDHIKARA,L.WANG,T.APPLEBY, JRNL AUTH 2 A.G.VILLASENOR,U.SCHMITZ,D.SHIVAKUMAR JRNL TITL EVALUATION OF FREE ENERGY CALCULATIONS FOR THE JRNL TITL 2 PRIORITIZATION OF MACROCYCLE SYNTHESIS. JRNL REF J.CHEM.INF.MODEL. V. 60 3489 2020 JRNL REFN ESSN 1549-960X JRNL PMID 32539379 JRNL DOI 10.1021/ACS.JCIM.0C00132 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 16568 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1658 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 25.1300 - 4.1200 0.97 1479 164 0.1477 0.1552 REMARK 3 2 4.1100 - 3.2700 0.96 1376 154 0.1634 0.1932 REMARK 3 3 3.2700 - 2.8600 0.90 1300 144 0.1854 0.2028 REMARK 3 4 2.8600 - 2.6000 0.78 1102 123 0.1835 0.2133 REMARK 3 5 2.6000 - 2.4100 0.78 1097 121 0.1711 0.2126 REMARK 3 6 2.4100 - 2.2700 0.82 1146 128 0.1592 0.1989 REMARK 3 7 2.2700 - 2.1500 0.83 1160 129 0.1595 0.1854 REMARK 3 8 2.1500 - 2.0600 0.85 1183 131 0.1643 0.2115 REMARK 3 9 2.0600 - 1.9800 0.89 1237 138 0.1598 0.2266 REMARK 3 10 1.9800 - 1.9100 0.90 1247 139 0.1561 0.2467 REMARK 3 11 1.9100 - 1.8500 0.92 1274 142 0.1800 0.2046 REMARK 3 12 1.8500 - 1.8000 0.94 1309 145 0.2092 0.2887 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) : 0.194 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.08 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 : 0.006 1282 REMARK 3 ANGLE : 0.846 1728 REMARK 3 CHIRALITY : 0.071 180 REMARK 3 PLANARITY : 0.004 230 REMARK 3 DIHEDRAL : 5.983 170 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 6X3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000249547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18908 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 57.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 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) : 0.08000 REMARK 200 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2CPL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM TRIS-HCL, PH 8.5, 2 MM DTT, 2 MM REMARK 280 EDTA, 20-35% PEG3350, 5% ETHANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 21.10100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.38450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.20300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.38450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.10100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.20300 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 165 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 LYS A 28 CE NZ REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 LYS A 131 CD CE NZ REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 LYS A 154 CD CE NZ REMARK 470 LYS A 155 CD CE NZ 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 60 -78.25 -139.10 REMARK 500 ASN A 71 12.35 -144.56 REMARK 500 LYS A 133 -70.88 -100.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: METHYL (3~{S})-1-[(2~{S})-2-[[(2~{S})-2-ACETAMIDO-3- REMARK 630 METHYL-BUTANOYL]AMINO]-3-(3-HYDROXYPHENYL)PROPANOYL]-1,2-DIAZINANE- REMARK 630 3-CARBOXYLATE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 ZXX A 400 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ACE VAL MTY UM7 REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZXX A 400 DBREF 6X3R A 1 165 UNP P62937 PPIA_HUMAN 1 165 SEQADV 6X3R GLY A -1 UNP P62937 EXPRESSION TAG SEQADV 6X3R HIS A 0 UNP P62937 EXPRESSION TAG SEQRES 1 A 167 GLY HIS MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA SEQRES 2 A 167 VAL ASP GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU SEQRES 3 A 167 PHE ALA ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG SEQRES 4 A 167 ALA LEU SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SEQRES 5 A 167 SER CYS PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN SEQRES 6 A 167 GLY GLY ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SEQRES 7 A 167 SER ILE TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE SEQRES 8 A 167 LEU LYS HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN SEQRES 9 A 167 ALA GLY PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS SEQRES 10 A 167 THR ALA LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL SEQRES 11 A 167 PHE GLY LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA SEQRES 12 A 167 MET GLU ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS SEQRES 13 A 167 LYS ILE THR ILE ALA ASP CYS GLY GLN LEU GLU HET ZXX A 400 32 HETNAM ZXX METHYL (3~{S})-1-[(2~{S})-2-[[(2~{S})-2-ACETAMIDO-3- HETNAM 2 ZXX METHYL-BUTANOYL]AMINO]-3-(3-HYDROXYPHENYL)PROPANOYL]- HETNAM 3 ZXX 1,2-DIAZINANE-3-CARBOXYLATE FORMUL 2 ZXX C22 H32 N4 O6 FORMUL 3 HOH *167(H2 O) HELIX 1 AA1 VAL A 29 GLY A 42 1 14 HELIX 2 AA2 THR A 119 ASP A 123 5 5 HELIX 3 AA3 GLY A 135 ARG A 144 1 10 SHEET 1 AA1 8 PHE A 53 ILE A 57 0 SHEET 2 AA1 8 MET A 61 GLY A 64 -1 O GLN A 63 N ARG A 55 SHEET 3 AA1 8 PHE A 112 CYS A 115 -1 O ILE A 114 N CYS A 62 SHEET 4 AA1 8 ILE A 97 MET A 100 -1 N ILE A 97 O CYS A 115 SHEET 5 AA1 8 VAL A 128 VAL A 132 -1 O GLY A 130 N LEU A 98 SHEET 6 AA1 8 GLU A 15 LEU A 24 -1 N GLU A 23 O LYS A 131 SHEET 7 AA1 8 THR A 5 VAL A 12 -1 N ILE A 10 O GLY A 18 SHEET 8 AA1 8 ILE A 156 GLN A 163 -1 O ASP A 160 N ASP A 9 SITE 1 AC1 17 ARG A 55 ILE A 57 PHE A 60 GLN A 63 SITE 2 AC1 17 GLY A 72 GLU A 86 ASN A 87 ALA A 101 SITE 3 AC1 17 ASN A 102 ALA A 103 GLN A 111 PHE A 113 SITE 4 AC1 17 HIS A 126 HOH A 501 HOH A 527 HOH A 573 SITE 5 AC1 17 HOH A 588 CRYST1 42.202 52.406 88.769 90.00 90.00 90.00 P 21 21 21 4 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 0.023696 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011265 0.00000