HEADER HYDROLASE/ANTIBIOTIC 10-JUN-19 6P9C TITLE OXA-48 CARBAPANEMASE, DORIPENEM COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLA OXA-48, BLAOXA-48, KPE71T_00045; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTIBIOTIC RESISTANCE, BETA-LACTAMASE, CARBAPENEMASE, DORUPENEM KEYWDS 2 COMPLEX, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SMITH,S.B.VAKULENKO REVDAT 2 09-OCT-19 6P9C 1 JRNL REVDAT 1 07-AUG-19 6P9C 0 JRNL AUTH C.A.SMITH,N.K.STEWART,M.TOTH,S.B.VAKULENKO JRNL TITL STRUCTURAL INSIGHTS INTO THE MECHANISM OF CARBAPENEMASE JRNL TITL 2 ACTIVITY OF THE OXA-48 BETA-LACTAMASE. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 63 2019 JRNL REFN ESSN 1098-6596 JRNL PMID 31358584 JRNL DOI 10.1128/AAC.01202-19 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 36.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 44388 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2254 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 36.5183 - 4.7843 0.99 2819 168 0.1779 0.2036 REMARK 3 2 4.7843 - 3.7988 0.98 2710 136 0.1551 0.1907 REMARK 3 3 3.7988 - 3.3189 1.00 2690 163 0.1888 0.2425 REMARK 3 4 3.3189 - 3.0156 0.97 2635 128 0.2049 0.2502 REMARK 3 5 3.0156 - 2.7996 0.99 2675 150 0.2104 0.2644 REMARK 3 6 2.7996 - 2.6346 1.00 2673 119 0.2056 0.2512 REMARK 3 7 2.6346 - 2.5027 0.99 2650 147 0.2016 0.2741 REMARK 3 8 2.5027 - 2.3937 0.97 2578 135 0.2032 0.2403 REMARK 3 9 2.3937 - 2.3016 0.99 2629 157 0.2029 0.2638 REMARK 3 10 2.3016 - 2.2222 0.98 2589 152 0.2281 0.2954 REMARK 3 11 2.2222 - 2.1527 0.99 2635 132 0.2060 0.2705 REMARK 3 12 2.1527 - 2.0912 1.00 2675 124 0.2018 0.2702 REMARK 3 13 2.0912 - 2.0361 0.96 2512 153 0.2051 0.3043 REMARK 3 14 2.0361 - 1.9865 0.97 2585 133 0.2087 0.2526 REMARK 3 15 1.9865 - 1.9413 0.98 2614 129 0.2448 0.2608 REMARK 3 16 1.9413 - 1.9000 0.94 2465 128 0.3250 0.3940 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.45 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6P9C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000242163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-19 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44627 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 38.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 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) : 1.94 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 : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MM CA2+, 5 MM CO2+, 5 MM CD2+, 20% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 36.30200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.59400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.37450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.59400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.30200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.37450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 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 ARG A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 LEU A 6 REMARK 465 SER A 7 REMARK 465 ALA A 8 REMARK 465 VAL A 9 REMARK 465 PHE A 10 REMARK 465 LEU A 11 REMARK 465 VAL A 12 REMARK 465 ALA A 13 REMARK 465 SER A 14 REMARK 465 ILE A 15 REMARK 465 ILE A 16 REMARK 465 GLY A 17 REMARK 465 MET A 18 REMARK 465 PRO A 19 REMARK 465 ALA A 20 REMARK 465 VAL A 21 REMARK 465 ALA A 22 REMARK 465 LYS A 23 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 VAL B 3 REMARK 465 LEU B 4 REMARK 465 ALA B 5 REMARK 465 LEU B 6 REMARK 465 SER B 7 REMARK 465 ALA B 8 REMARK 465 VAL B 9 REMARK 465 PHE B 10 REMARK 465 LEU B 11 REMARK 465 VAL B 12 REMARK 465 ALA B 13 REMARK 465 SER B 14 REMARK 465 ILE B 15 REMARK 465 ILE B 16 REMARK 465 GLY B 17 REMARK 465 MET B 18 REMARK 465 PRO B 19 REMARK 465 ALA B 20 REMARK 465 VAL B 21 REMARK 465 ALA B 22 REMARK 465 LYS B 23 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 GLU A 24 CG CD OE1 OE2 REMARK 470 GLU B 24 CG CD OE1 OE2 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 ALA A 69 -133.70 50.73 REMARK 500 TRP A 95 -9.81 -51.79 REMARK 500 ASP A 96 46.27 37.78 REMARK 500 GLN A 98 117.56 -33.12 REMARK 500 ARG A 100 73.36 -29.35 REMARK 500 ASP A 101 -65.17 49.53 REMARK 500 ASN A 106 40.59 -109.65 REMARK 500 SER A 118 -77.50 73.26 REMARK 500 VAL A 119 102.90 56.09 REMARK 500 SER A 155 11.63 -156.24 REMARK 500 ASP A 159 16.46 -144.54 REMARK 500 ALA B 69 -134.27 49.93 REMARK 500 ASN B 106 53.27 -91.83 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 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 OE2 REMARK 620 2 GLU A 256 OE1 72.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 307 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 OE2 REMARK 620 2 HIS A 38 NE2 98.5 REMARK 620 3 GLU A 256 OE1 77.7 102.9 REMARK 620 4 GLU A 256 OE2 113.6 128.1 50.8 REMARK 620 5 GLU A 125 OE1 120.6 47.9 68.6 80.3 REMARK 620 6 GLU A 125 OE2 117.6 46.6 67.6 81.9 3.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 306 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 154 OD1 REMARK 620 2 ASP A 154 OD2 42.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 143 OD1 REMARK 620 2 GLU B 147 OE1 61.9 REMARK 620 3 GLU B 147 OE2 99.4 48.3 REMARK 620 4 HOH B 446 O 92.0 108.1 77.9 REMARK 620 5 HOH B 452 O 161.5 99.9 67.4 97.5 REMARK 620 6 ASP A 143 OD1 60.6 83.1 75.0 33.2 123.9 REMARK 620 7 GLU A 147 OE1 61.5 85.7 77.1 31.5 124.0 2.6 REMARK 620 8 HOH A 413 O 123.9 172.2 123.9 67.7 74.6 95.3 92.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 306 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 143 OD1 REMARK 620 2 HOH B 401 O 85.8 REMARK 620 3 HOH B 404 O 87.0 165.1 REMARK 620 4 GLU A 147 OE1 32.0 94.4 72.8 REMARK 620 5 GLU A 147 OE2 30.7 95.6 71.9 2.0 REMARK 620 6 HOH A 486 O 159.2 90.5 91.6 128.5 130.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4J6 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O6P A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4J6 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O6P B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 306 DBREF 6P9C A 1 265 UNP Q6XEC0 Q6XEC0_KLEPN 1 265 DBREF 6P9C B 1 265 UNP Q6XEC0 Q6XEC0_KLEPN 1 265 SEQRES 1 A 265 MET ARG VAL LEU ALA LEU SER ALA VAL PHE LEU VAL ALA SEQRES 2 A 265 SER ILE ILE GLY MET PRO ALA VAL ALA LYS GLU TRP GLN SEQRES 3 A 265 GLU ASN LYS SER TRP ASN ALA HIS PHE THR GLU HIS LYS SEQRES 4 A 265 SER GLN GLY VAL VAL VAL LEU TRP ASN GLU ASN LYS GLN SEQRES 5 A 265 GLN GLY PHE THR ASN ASN LEU LYS ARG ALA ASN GLN ALA SEQRES 6 A 265 PHE LEU PRO ALA SER THR PHE LYS ILE PRO ASN SER LEU SEQRES 7 A 265 ILE ALA LEU ASP LEU GLY VAL VAL LYS ASP GLU HIS GLN SEQRES 8 A 265 VAL PHE LYS TRP ASP GLY GLN THR ARG ASP ILE ALA THR SEQRES 9 A 265 TRP ASN ARG ASP HIS ASN LEU ILE THR ALA MET LYS TYR SEQRES 10 A 265 SER VAL VAL PRO VAL TYR GLN GLU PHE ALA ARG GLN ILE SEQRES 11 A 265 GLY GLU ALA ARG MET SER LYS MET LEU HIS ALA PHE ASP SEQRES 12 A 265 TYR GLY ASN GLU ASP ILE SER GLY ASN VAL ASP SER PHE SEQRES 13 A 265 TRP LEU ASP GLY GLY ILE ARG ILE SER ALA THR GLU GLN SEQRES 14 A 265 ILE SER PHE LEU ARG LYS LEU TYR HIS ASN LYS LEU HIS SEQRES 15 A 265 VAL SER GLU ARG SER GLN ARG ILE VAL LYS GLN ALA MET SEQRES 16 A 265 LEU THR GLU ALA ASN GLY ASP TYR ILE ILE ARG ALA LYS SEQRES 17 A 265 THR GLY TYR SER THR ARG ILE GLU PRO LYS ILE GLY TRP SEQRES 18 A 265 TRP VAL GLY TRP VAL GLU LEU ASP ASP ASN VAL TRP PHE SEQRES 19 A 265 PHE ALA MET ASN MET ASP MET PRO THR SER ASP GLY LEU SEQRES 20 A 265 GLY LEU ARG GLN ALA ILE THR LYS GLU VAL LEU LYS GLN SEQRES 21 A 265 GLU LYS ILE ILE PRO SEQRES 1 B 265 MET ARG VAL LEU ALA LEU SER ALA VAL PHE LEU VAL ALA SEQRES 2 B 265 SER ILE ILE GLY MET PRO ALA VAL ALA LYS GLU TRP GLN SEQRES 3 B 265 GLU ASN LYS SER TRP ASN ALA HIS PHE THR GLU HIS LYS SEQRES 4 B 265 SER GLN GLY VAL VAL VAL LEU TRP ASN GLU ASN LYS GLN SEQRES 5 B 265 GLN GLY PHE THR ASN ASN LEU LYS ARG ALA ASN GLN ALA SEQRES 6 B 265 PHE LEU PRO ALA SER THR PHE LYS ILE PRO ASN SER LEU SEQRES 7 B 265 ILE ALA LEU ASP LEU GLY VAL VAL LYS ASP GLU HIS GLN SEQRES 8 B 265 VAL PHE LYS TRP ASP GLY GLN THR ARG ASP ILE ALA THR SEQRES 9 B 265 TRP ASN ARG ASP HIS ASN LEU ILE THR ALA MET LYS TYR SEQRES 10 B 265 SER VAL VAL PRO VAL TYR GLN GLU PHE ALA ARG GLN ILE SEQRES 11 B 265 GLY GLU ALA ARG MET SER LYS MET LEU HIS ALA PHE ASP SEQRES 12 B 265 TYR GLY ASN GLU ASP ILE SER GLY ASN VAL ASP SER PHE SEQRES 13 B 265 TRP LEU ASP GLY GLY ILE ARG ILE SER ALA THR GLU GLN SEQRES 14 B 265 ILE SER PHE LEU ARG LYS LEU TYR HIS ASN LYS LEU HIS SEQRES 15 B 265 VAL SER GLU ARG SER GLN ARG ILE VAL LYS GLN ALA MET SEQRES 16 B 265 LEU THR GLU ALA ASN GLY ASP TYR ILE ILE ARG ALA LYS SEQRES 17 B 265 THR GLY TYR SER THR ARG ILE GLU PRO LYS ILE GLY TRP SEQRES 18 B 265 TRP VAL GLY TRP VAL GLU LEU ASP ASP ASN VAL TRP PHE SEQRES 19 B 265 PHE ALA MET ASN MET ASP MET PRO THR SER ASP GLY LEU SEQRES 20 B 265 GLY LEU ARG GLN ALA ILE THR LYS GLU VAL LEU LYS GLN SEQRES 21 B 265 GLU LYS ILE ILE PRO HET 4J6 A 301 27 HET O6P A 302 27 HET CL A 303 1 HET CL A 304 1 HET CA A 305 1 HET CA A 306 1 HET CD A 307 1 HET 4J6 B 301 27 HET O6P B 302 27 HET CL B 303 1 HET CL B 304 1 HET CA B 305 1 HET CD B 306 1 HETNAM 4J6 (4R,5S)-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL- HETNAM 2 4J6 3-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3- HETNAM 3 4J6 YL}SULFANYL)-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID HETNAM O6P DORIPENEM HETNAM CL CHLORIDE ION HETNAM CA CALCIUM ION HETNAM CD CADMIUM ION HETSYN 4J6 DORIPENEM(OPEN FORM, PYRROLINE TAUTOMER FORM 1, SP2 HETSYN 2 4J6 CONNECTION TO THIO) HETSYN O6P (4R,5S,6S)-6-[(1R)-1-HYDROXYETHYL]-4-METHYL-7-OXO-3- HETSYN 2 O6P ({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3- HETSYN 3 O6P YL}SULFANYL)-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2- HETSYN 4 O6P CARBOXYLIC ACID FORMUL 3 4J6 2(C15 H26 N4 O6 S2) FORMUL 4 O6P 2(C15 H24 N4 O6 S2) FORMUL 5 CL 4(CL 1-) FORMUL 7 CA 3(CA 2+) FORMUL 9 CD 2(CD 2+) FORMUL 16 HOH *181(H2 O) HELIX 1 AA1 TRP A 31 GLU A 37 1 7 HELIX 2 AA2 ASN A 58 ASN A 63 1 6 HELIX 3 AA3 PRO A 68 THR A 71 5 4 HELIX 4 AA4 PHE A 72 LEU A 83 1 12 HELIX 5 AA5 ILE A 102 ASN A 106 5 5 HELIX 6 AA6 ASN A 110 SER A 118 1 9 HELIX 7 AA7 VAL A 119 ASP A 143 1 25 HELIX 8 AA8 SER A 155 GLY A 160 1 6 HELIX 9 AA9 ALA A 166 HIS A 178 1 13 HELIX 10 AB1 SER A 184 MET A 195 1 12 HELIX 11 AB2 THR A 243 LEU A 247 5 5 HELIX 12 AB3 GLY A 248 GLU A 261 1 14 HELIX 13 AB4 TRP B 31 HIS B 38 1 8 HELIX 14 AB5 ASN B 58 ASN B 63 1 6 HELIX 15 AB6 PRO B 68 THR B 71 5 4 HELIX 16 AB7 PHE B 72 LEU B 83 1 12 HELIX 17 AB8 ILE B 102 ASN B 106 5 5 HELIX 18 AB9 ASN B 110 TYR B 117 1 8 HELIX 19 AC1 VAL B 119 GLY B 131 1 13 HELIX 20 AC2 GLY B 131 ASP B 143 1 13 HELIX 21 AC3 SER B 155 GLY B 160 1 6 HELIX 22 AC4 ALA B 166 HIS B 178 1 13 HELIX 23 AC5 SER B 184 MET B 195 1 12 HELIX 24 AC6 THR B 243 LEU B 247 5 5 HELIX 25 AC7 GLY B 248 GLU B 261 1 14 SHEET 1 AA1 7 TRP A 25 GLU A 27 0 SHEET 2 AA1 7 GLN A 53 THR A 56 1 O GLY A 54 N GLN A 26 SHEET 3 AA1 7 GLY A 42 ASN A 48 -1 N LEU A 46 O PHE A 55 SHEET 4 AA1 7 VAL A 232 ASP A 240 -1 O ASN A 238 N VAL A 43 SHEET 5 AA1 7 ILE A 219 GLU A 227 -1 N GLY A 224 O PHE A 235 SHEET 6 AA1 7 ILE A 204 SER A 212 -1 N ILE A 204 O GLU A 227 SHEET 7 AA1 7 LEU A 196 ALA A 199 -1 N GLU A 198 O ILE A 205 SHEET 1 AA2 2 ALA A 65 PHE A 66 0 SHEET 2 AA2 2 ILE A 164 SER A 165 -1 O ILE A 164 N PHE A 66 SHEET 1 AA3 7 TRP B 25 GLU B 27 0 SHEET 2 AA3 7 GLN B 53 THR B 56 1 O GLY B 54 N GLN B 26 SHEET 3 AA3 7 GLY B 42 ASN B 48 -1 N ASN B 48 O GLN B 53 SHEET 4 AA3 7 VAL B 232 ASP B 240 -1 O ASN B 238 N VAL B 43 SHEET 5 AA3 7 ILE B 219 GLU B 227 -1 N VAL B 226 O TRP B 233 SHEET 6 AA3 7 ILE B 204 SER B 212 -1 N ILE B 204 O GLU B 227 SHEET 7 AA3 7 LEU B 196 ALA B 199 -1 N GLU B 198 O ILE B 205 SHEET 1 AA4 2 ALA B 65 PHE B 66 0 SHEET 2 AA4 2 ILE B 164 SER B 165 -1 O ILE B 164 N PHE B 66 LINK OE2 GLU A 37 CA CA A 305 1555 1555 2.31 LINK OE2 GLU A 37 CD CD A 307 1555 1555 2.52 LINK NE2 HIS A 38 CD CD A 307 1555 1555 2.39 LINK OG SER A 70 CAJ 4J6 A 301 1555 1555 1.38 LINK OD1 ASP A 154 CA CA A 306 1555 1555 3.15 LINK OD2 ASP A 154 CA CA A 306 1555 1555 2.83 LINK OE1 GLU A 256 CA CA A 305 1555 1555 3.01 LINK OE1 GLU A 256 CD CD A 307 1555 1555 2.58 LINK OE2 GLU A 256 CD CD A 307 1555 1555 2.59 LINK OD1 ASP B 143 CA CA B 305 1555 1555 2.87 LINK OD1 ASP B 143 CD CD B 306 1555 1555 2.51 LINK OE1 GLU B 147 CA CA B 305 1555 1555 2.29 LINK OE2 GLU B 147 CA CA B 305 1555 1555 2.86 LINK CA CA B 305 O HOH B 446 1555 1555 2.27 LINK CA CA B 305 O HOH B 452 1555 1555 2.14 LINK CD CD B 306 O HOH B 401 1555 1555 2.64 LINK CD CD B 306 O HOH B 404 1555 1555 2.46 LINK OE1 GLU A 125 CD CD A 307 1555 4445 2.60 LINK OE2 GLU A 125 CD CD A 307 1555 4445 2.55 LINK OD1 ASP A 143 CA CA B 305 1555 3544 2.31 LINK OE1 GLU A 147 CD CD B 306 1555 3544 2.42 LINK OE1 GLU A 147 CA CA B 305 1555 3544 2.35 LINK OE2 GLU A 147 CD CD B 306 1555 3544 2.53 LINK CA CA B 305 O HOH A 413 1555 3554 2.85 LINK CD CD B 306 O HOH A 486 1555 3554 2.64 CISPEP 1 GLU A 216 PRO A 217 0 1.11 CISPEP 2 GLU B 216 PRO B 217 0 -1.12 SITE 1 AC1 11 ALA A 69 SER A 70 SER A 118 GLU A 132 SITE 2 AC1 11 LEU A 158 THR A 209 GLY A 210 TYR A 211 SITE 3 AC1 11 LEU A 247 ARG A 250 HOH A 419 SITE 1 AC2 9 ASN A 48 LYS A 51 LEU A 228 ASP A 230 SITE 2 AC2 9 ASN A 231 TRP A 233 GLU A 261 LYS A 262 SITE 3 AC2 9 ILE A 263 SITE 1 AC3 2 LYS A 73 TRP A 157 SITE 1 AC4 2 ARG A 206 ARG B 206 SITE 1 AC5 4 HIS A 34 GLU A 37 GLU A 256 CD A 307 SITE 1 AC6 1 ASP A 154 SITE 1 AC7 5 GLU A 37 HIS A 38 GLU A 125 GLU A 256 SITE 2 AC7 5 CA A 305 SITE 1 AC8 12 ALA B 69 SER B 70 SER B 118 LEU B 158 SITE 2 AC8 12 LYS B 208 THR B 209 GLY B 210 TYR B 211 SITE 3 AC8 12 SER B 244 LEU B 247 ARG B 250 HOH B 464 SITE 1 AC9 9 ASN B 48 LYS B 51 LEU B 228 ASP B 230 SITE 2 AC9 9 ASN B 231 TRP B 233 GLU B 261 LYS B 262 SITE 3 AC9 9 ILE B 263 SITE 1 AD1 2 LYS B 73 TRP B 157 SITE 1 AD2 7 ASP A 143 GLU A 147 HOH A 413 ASP B 143 SITE 2 AD2 7 GLU B 147 HOH B 446 HOH B 452 SITE 1 AD3 7 GLU A 147 HOH A 486 ASP B 143 GLU B 147 SITE 2 AD3 7 HOH B 401 HOH B 404 HOH B 423 CRYST1 72.604 76.749 101.188 90.00 90.00 90.00 P 21 21 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 0.013773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009883 0.00000