Structure of PDB 3bfg Chain B Binding Site BS01

Receptor Information

>3bfg Chain B (length=262) Species: 67826 (Citrobacter sedlakii)

VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMT
AAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAAT
LQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGD
ERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLP
AHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDV
LAAAAKIVTEGK

Ligand information

• Ligand ID: MER
• InChI: InChI=1S/C17H27N3O5S/c1-8-13(11(7-21)9(2)22)19-14(17(24)25)15(8)26-10-5-12(18-6-10)16(23)20(3)4/h7-13,18-19,22H,5-6H2,1-4H3,(H,24,25)/t8-,9-,10+,11-,12+,13-/m1/s1
• InChIKey: DYQHXZPAIVAJRU-HTXLXMOSSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC1C(NC(=C1SC2CC(NC2)C(=O)N(C)C)C(=O)O)C(C=O)C(C)O
  CACTVS 3.370: C[CH](O)[CH](C=O)[CH]1NC(=C(S[CH]2CN[CH](C2)C(=O)N(C)C)[CH]1C)C(O)=O
  CACTVS 3.370: C[C@@H](O)[C@@H](C=O)[C@@H]1NC(=C(S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)C(O)=O
  ACDLabs 12.01: O=C(O)C2=C(SC1CC(C(=O)N(C)C)NC1)C(C(N2)C(C=O)C(O)C)C
  OpenEye OEToolkits 1.7.6: C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C)C)C(=O)O)[C@H](C=O)[C@@H](C)O
• Formula: C17 H27 N3 O5 S
• Name: (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid;
  Meropenem, bound form
• ZINC: ZINC000103547705
• PDB chain: 3bfg Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3bfg Crystallization and preliminary X-ray diffraction study of the class A beta-lactamase SED-1 and its mutant SED-G238C from Citrobacter sedlakii
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): S70 W105 S130 N132 T216 T235 G236 A237
• Binding residue (residue number reindexed from 1): S44 W79 S104 N106 T190 T209 G210 A211
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S130 E166 K234 A237
• Catalytic site (residue number reindexed from 1): S44 K47 S104 E140 K208 A211
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0008800 beta-lactamase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0017001 antibiotic catabolic process
• GO:0030655 beta-lactam antibiotic catabolic process
• GO:0046677 response to antibiotic

External links

• PDB: RCSB:3bfg, PDBe:3bfg, PDBj:3bfg
• PDBsum: 3bfg
• UniProt: Q93PQ0