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(-) Description

Title :  ATOMIC RESOLUTION X-RAY CRYSTAL STRUCTURE OF A RUTHENOCENE CONJUGATED BETA-LACTAM ANTIBIOTIC IN COMPLEX WITH CTX-M-14 E166A BETA-LACTAMASE
 
Authors :  E. M. Lewandowski, Y. Chen
Date :  30 Jan 15  (Deposition) - 18 Mar 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Lactamase Organometallic Ruthenocene Ctx-M-14, Hydrolase- Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Lewandowski, J. Skiba, N. J. Torelli, A. Rajnisz, J. Solecka, K. Kowalski, Y. Chen
Antibacterial Properties And Atomic Resolution X-Ray Comple Crystal Structure Of A Ruthenocene Conjugated Beta-Lactam Antibiotic.
Chem. Commun. (Camb. ) V. 51 6186 2015
PubMed-ID: 25753149  |  Reference-DOI: 10.1039/C5CC00904A

(-) Compounds

Molecule 1 - CTX-M-14 CLASS A BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 29-291
    Gene: BLACTX-M-14, BETA-LACTAMASE CTX-M-14, BLA-CTX-M-14A, BLACTX-M- 14A, BLACTX-M-14B, BLACTX-M-14C, BLACTX-M-27B, BLATOHO-3, BLAUOE-2, CTX-M-14, ETN48_P0088, PCT_085, PHK01_011
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1JSC3Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[CARBOXY(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
2JSD2Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
3JSE1Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[CARBOXY(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
4K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1JSC2Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[CARBOXY(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
2JSD1Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
3JSE1Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[CARBOXY(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
4K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1JSC1Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[CARBOXY(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
2JSD1Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
3JSE-1Ligand/Ion[(1,2,3,4,5-ETA)-1-(4-{[CARBOXY(4-CARBOXY-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL)METHYL]AMINO}-4-OXOBUTANOYL)CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]RUTHENIUM
4K-1Ligand/IonPOTASSIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:238 , HOH A:548 , HOH A:550 , HOH A:567 , HOH A:643 , HOH A:651binding site for residue K A 301
2AC2SOFTWARESER A:70 , ASN A:104 , SER A:130 , ASN A:132 , PRO A:167 , ASN A:170 , LYS A:234 , THR A:235 , GLY A:236 , SER A:237 , GLY A:238 , ASP A:240 , ARG A:256 , ARG A:276 , HOH A:558 , HOH A:567 , HOH A:578 , HOH A:643binding site for residue JSD A 302
3AC3SOFTWAREGLN A:31 , LYS A:32 , ALA A:35 , LYS A:82 , GLU A:85 , THR A:86 , ALA A:154 , GLN A:192 , HIS A:197 , ALA A:198 , HOH A:406 , HOH A:459 , HOH A:594 , GLY B:143 , GLY B:146 , GLY B:147 , HOH B:455 , HOH B:485binding site for residue JSC A 303
4AC4SOFTWAREASN A:54 , GLN A:56 , ARG A:184 , GLN A:188 , ARG A:191 , JSC A:305 , HOH A:620 , GLN B:83 , GLN B:87 , ALA B:140 , GLN B:141 , LEU B:142 , GLY B:143 , ALA B:150 , HOH B:500binding site for residue JSE A 304
5AC5SOFTWAREASN A:54 , JSE A:304 , LYS B:82 , GLN B:83 , ALA B:154binding site for residue JSC A 305
6AC6SOFTWAREGLY B:238 , HOH B:574 , HOH B:575 , HOH B:592 , HOH B:680binding site for residue K B 301
7AC7SOFTWAREASN B:104 , SER B:130 , ASN B:132 , PRO B:167 , ASN B:170 , LYS B:234 , THR B:235 , GLY B:236 , SER B:237 , GLY B:238 , ASP B:240 , ARG B:256 , ARG B:276 , HOH B:569 , HOH B:592 , HOH B:635 , HOH B:685binding site for residue JSD B 302
8AC8SOFTWAREILE B:108 , GLU B:121 , TYR B:129 , HOH B:667binding site for residue JSC B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XXR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:166 -Pro A:167
2Ala B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XXR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XXR)

(-) Exons   (0, 0)

(no "Exon" information available for 4XXR)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee....eeeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xxr A  26 TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTAPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    35        45        55 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                          57|                                                                                                                                                                                238|         252|                                    
                                                           59                                                                                                                                                                                 240          254                                    


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xxr B  28 AVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTAPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    37        47        57|       68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238|      249  ||   260       270       280       290
                                                        57|                                                                                                                                                                                238|         252|                                    
                                                         59                                                                                                                                                                                 240          254
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4XXR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XXR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XXR)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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