Structure of PDB 5ypm Chain A

Receptor sequence
>5ypmA (length=228) Species: 562 (Escherichia coli) [Search protein sequence]
DQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTA
WTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYAN
ALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSD
NITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPK
ASMIVMSHSAPDSRAAITHTARMADKLR
3D structure
PDB5ypm The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
ChainA
Resolution2.15 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) H120 H122 D124 H189 C208 K211 N220 H250
Catalytic site (residue number reindexed from 1) H78 H80 D82 H147 C166 K169 N178 H208
Enzyme Commision number 3.5.2.6: beta-lactamase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN A H120 H122 H189 H78 H80 H147
BS02 ZN A D124 C208 H250 D82 C166 H208
BS03 8YL A H122 D124 H189 C208 K211 N220 H250 H80 D82 H147 C166 K169 N178 H208
BS04 8YL A G69 F70 G27 F28
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:5ypm, PDBe:5ypm, PDBj:5ypm
PDBsum5ypm
PubMed29269938
UniProtE5KIY2

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