HEADER LYASE 14-JUL-16 5GMN TITLE CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH TITLE 2 POLMACOXIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBONATE DEHYDRATASE II,CARBONIC ANHYDRASE C,CAC,CARBONIC COMPND 5 ANHYDRASE II,CA-II; COMPND 6 EC: 4.2.1.1; 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: CA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS LYASE, INHIBITOR, COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.T.KIM,K.Y.HWANG REVDAT 3 08-NOV-23 5GMN 1 REMARK REVDAT 2 20-JUN-18 5GMN 1 COMPND REVDAT 1 24-MAY-17 5GMN 0 JRNL AUTH H.T.KIM,H.CHA,K.Y.HWANG JRNL TITL STRUCTURAL INSIGHT INTO THE INHIBITION OF CARBONIC ANHYDRASE JRNL TITL 2 BY THE COX-2-SELECTIVE INHIBITOR POLMACOXIB (CG100649). JRNL REF BIOCHEM. BIOPHYS. RES. V. 478 1 2016 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 27475498 JRNL DOI 10.1016/J.BBRC.2016.07.114 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 20744 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1068 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 36.0757 - 3.5991 0.98 2605 124 0.1497 0.1919 REMARK 3 2 3.5991 - 2.8571 1.00 2503 128 0.1548 0.1877 REMARK 3 3 2.8571 - 2.4960 1.00 2483 149 0.1680 0.2337 REMARK 3 4 2.4960 - 2.2678 1.00 2480 122 0.1602 0.1875 REMARK 3 5 2.2678 - 2.1053 1.00 2435 136 0.1506 0.1997 REMARK 3 6 2.1053 - 1.9812 1.00 2450 136 0.1519 0.2113 REMARK 3 7 1.9812 - 1.8820 0.99 2426 126 0.1528 0.2037 REMARK 3 8 1.8820 - 1.8001 0.95 2294 147 0.1501 0.2189 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 2136 REMARK 3 ANGLE : 1.222 2904 REMARK 3 CHIRALITY : 0.049 301 REMARK 3 PLANARITY : 0.006 376 REMARK 3 DIHEDRAL : 15.579 780 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 5GMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300001073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20744 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.6000 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 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: NULL REMARK 200 STARTING MODEL: 1OQ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 28% PEGMME2K, REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 20.92350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.56650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.76550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.56650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.92350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.76550 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 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 O HOH A 441 O HOH A 649 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 ASN A 243 52.07 -95.96 REMARK 500 LYS A 251 -132.79 55.38 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 96 NE2 105.6 REMARK 620 3 HIS A 119 ND1 112.8 96.1 REMARK 620 4 949 A 302 N22 105.9 112.7 122.5 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 ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 949 A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GMM RELATED DB: PDB DBREF 5GMN A 1 260 UNP P00918 CAH2_HUMAN 1 260 SEQRES 1 A 260 MET SER HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO SEQRES 2 A 260 GLU HIS TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU SEQRES 3 A 260 ARG GLN SER PRO VAL ASP ILE ASP THR HIS THR ALA LYS SEQRES 4 A 260 TYR ASP PRO SER LEU LYS PRO LEU SER VAL SER TYR ASP SEQRES 5 A 260 GLN ALA THR SER LEU ARG ILE LEU ASN ASN GLY HIS ALA SEQRES 6 A 260 PHE ASN VAL GLU PHE ASP ASP SER GLN ASP LYS ALA VAL SEQRES 7 A 260 LEU LYS GLY GLY PRO LEU ASP GLY THR TYR ARG LEU ILE SEQRES 8 A 260 GLN PHE HIS PHE HIS TRP GLY SER LEU ASP GLY GLN GLY SEQRES 9 A 260 SER GLU HIS THR VAL ASP LYS LYS LYS TYR ALA ALA GLU SEQRES 10 A 260 LEU HIS LEU VAL HIS TRP ASN THR LYS TYR GLY ASP PHE SEQRES 11 A 260 GLY LYS ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU SEQRES 12 A 260 GLY ILE PHE LEU LYS VAL GLY SER ALA LYS PRO GLY LEU SEQRES 13 A 260 GLN LYS VAL VAL ASP VAL LEU ASP SER ILE LYS THR LYS SEQRES 14 A 260 GLY LYS SER ALA ASP PHE THR ASN PHE ASP PRO ARG GLY SEQRES 15 A 260 LEU LEU PRO GLU SER LEU ASP TYR TRP THR TYR PRO GLY SEQRES 16 A 260 SER LEU THR THR PRO PRO LEU LEU GLU CYS VAL THR TRP SEQRES 17 A 260 ILE VAL LEU LYS GLU PRO ILE SER VAL SER SER GLU GLN SEQRES 18 A 260 VAL LEU LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY SEQRES 19 A 260 GLU PRO GLU GLU LEU MET VAL ASP ASN TRP ARG PRO ALA SEQRES 20 A 260 GLN PRO LEU LYS ASN ARG GLN ILE LYS ALA SER PHE LYS HET ZN A 301 1 HET 949 A 302 25 HETNAM ZN ZINC ION HETNAM 949 4-[3-(3-FLUOROPHENYL)-5,5-DIMETHYL-4-OXIDANYLIDENE- HETNAM 2 949 FURAN-2-YL]BENZENESULFONAMIDE HETSYN 949 POLMACOXIB FORMUL 2 ZN ZN 2+ FORMUL 3 949 C18 H16 F N O4 S FORMUL 4 HOH *282(H2 O) HELIX 1 AA1 HIS A 15 ASP A 19 5 5 HELIX 2 AA2 PHE A 20 GLY A 25 5 6 HELIX 3 AA3 LYS A 126 GLY A 128 5 3 HELIX 4 AA4 ASP A 129 VAL A 134 1 6 HELIX 5 AA5 LYS A 153 GLY A 155 5 3 HELIX 6 AA6 LEU A 156 LEU A 163 1 8 HELIX 7 AA7 ASP A 164 LYS A 167 5 4 HELIX 8 AA8 ASP A 179 LEU A 184 5 6 HELIX 9 AA9 SER A 218 ARG A 226 1 9 SHEET 1 AA1 2 ASP A 32 ILE A 33 0 SHEET 2 AA1 2 THR A 108 VAL A 109 1 O THR A 108 N ILE A 33 SHEET 1 AA210 LYS A 39 TYR A 40 0 SHEET 2 AA210 LYS A 256 ALA A 257 1 O ALA A 257 N LYS A 39 SHEET 3 AA210 TYR A 190 GLY A 195 -1 N THR A 192 O LYS A 256 SHEET 4 AA210 VAL A 206 LEU A 211 -1 O VAL A 206 N GLY A 195 SHEET 5 AA210 LEU A 140 VAL A 149 1 N LEU A 140 O THR A 207 SHEET 6 AA210 ALA A 116 ASN A 124 -1 N LEU A 118 O ILE A 145 SHEET 7 AA210 GLY A 86 TRP A 97 -1 N HIS A 94 O HIS A 119 SHEET 8 AA210 PHE A 66 PHE A 70 -1 N VAL A 68 O PHE A 93 SHEET 9 AA210 SER A 56 ASN A 61 -1 N LEU A 57 O GLU A 69 SHEET 10 AA210 SER A 172 ASP A 174 -1 O ALA A 173 N ILE A 59 SHEET 1 AA3 6 LYS A 45 SER A 50 0 SHEET 2 AA3 6 VAL A 78 GLY A 82 -1 O LYS A 80 N SER A 48 SHEET 3 AA3 6 GLY A 86 TRP A 97 -1 O TYR A 88 N LEU A 79 SHEET 4 AA3 6 ALA A 116 ASN A 124 -1 O HIS A 119 N HIS A 94 SHEET 5 AA3 6 LEU A 140 VAL A 149 -1 O ILE A 145 N LEU A 118 SHEET 6 AA3 6 ILE A 215 VAL A 217 1 O ILE A 215 N PHE A 146 LINK NE2 HIS A 94 ZN ZN A 301 1555 1555 2.04 LINK NE2 HIS A 96 ZN ZN A 301 1555 1555 2.09 LINK ND1 HIS A 119 ZN ZN A 301 1555 1555 2.09 LINK ZN ZN A 301 N22 949 A 302 1555 1555 1.93 CISPEP 1 SER A 29 PRO A 30 0 -0.53 CISPEP 2 PRO A 200 PRO A 201 0 11.81 SITE 1 AC1 4 HIS A 94 HIS A 96 HIS A 119 949 A 302 SITE 1 AC2 11 ILE A 91 HIS A 94 HIS A 96 HIS A 119 SITE 2 AC2 11 VAL A 121 PHE A 130 LEU A 197 THR A 198 SITE 3 AC2 11 THR A 199 TRP A 208 ZN A 301 CRYST1 41.847 73.531 71.133 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 0.023897 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013600 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014058 0.00000