Structure of PDB 5toy Chain B Binding Site BS03

Receptor Information

>5toy Chain B (length=261) Species: 562 (Escherichia coli)

SAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAA
AAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAAL
QYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTAPTLNTAIPGDP
RDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPT
SWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVL
ASAARIIAEGL

Ligand information

• Ligand ID: JSD
• InChI: InChI=1S/C16H21N2O4S.C5H5.Ru/c1-16(2)14(15(21)22)18-13(23-16)9-17-12(20)8-7-11(19)10-5-3-4-6-10;1-2-4-5-3-1;/h3-6,13-14,18H,7-9H2,1-2H3,(H,17,20)(H,21,22);1-5H;/t13-,14+;;/m1../s1
• InChIKey: JRWKHIBMJXULTB-BQFBZIMZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC1([C@@H](N[C@H](S1)CNC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12)C(=O)O)C
  CACTVS 3.385: CC1(C)S[CH](CNC(=O)CCC(=O)C23[Ru]|4|5|6|7|8|9|%10(|C%11C|4C|5C|6C|7%11)|C(C|8C2|9)C3|%10)N[CH]1C(O)=O
  OpenEye OEToolkits 1.7.6: CC1(C(NC(S1)CNC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12)C(=O)O)C
  CACTVS 3.385: CC1(C)S[C@H](CNC(=O)CCC(=O)C23[Ru]|4|5|6|7|8|9|%10(|C%11C|4C|5C|6C|7%11)|C(C|8C2|9)C3|%10)N[C@H]1C(O)=O
  ACDLabs 12.01: O=C(NCC1SC(C(N1)C(=O)O)(C)C)CCC(=O)C2%11C8C9C%10C2[Ru]865489%10%11C3C7C6C5C34
• Formula: C21 H17 N2 O4 Ru S
• Name: [(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
• PDB chain: 5toy Chain B Residue 306

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5toy Mechanisms of proton relay and product release by Class A beta-lactamase at ultrahigh resolution.
• Resolution: 1.3 Å
• Binding residue (original residue number in PDB): N104 Y105 S130 P167 N170 T171 T235 G236 S237 D240
• Binding residue (residue number reindexed from 1): N77 Y78 S103 P140 N143 T144 T208 G209 S210 D212
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S130 A166 K234 S237
• Catalytic site (residue number reindexed from 1): S43 K46 S103 A139 K207 S210
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0008800 beta-lactamase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

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

External links

• PDB: RCSB:5toy, PDBe:5toy, PDBj:5toy
• PDBsum: 5toy
• PubMed: 29095570
• UniProt: Q9L5C7