Structure of PDB 5ypk Chain D

Receptor sequence
>5ypkD (length=229) Species: 562 (Escherichia coli) [Search protein sequence]
GDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDT
AWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYA
NALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTS
DNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFP
KASMIVMSHSAPDSRAAITHTARMADKLR
3D structure
PDB5ypk The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
ChainD
Resolution2.0 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) H79 H81 D83 H148 C167 K170 N179 H209
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 D H120 H122 H189 H79 H81 H148
BS02 ZN D D124 C208 H250 D83 C167 H209
BS03 HIW D W93 H122 D124 H189 K211 G219 N220 H250 W52 H81 D83 H148 K170 G178 N179 H209
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:5ypk, PDBe:5ypk, PDBj:5ypk
PDBsum5ypk
PubMed29269938
UniProtE5KIY2

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