Structure of PDB 6d1d Chain A

Receptor sequence
>6d1dA (length=229) Species: 573 (Klebsiella pneumoniae) [Search protein sequence]
GDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDT
AWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYA
NALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTS
DNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFP
KASMIVMSHSAPDSRAAITHTARMADKLR
3D structure
PDB6d1d Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
ChainA
Resolution1.4 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 A H120 H122 H189 H79 H81 H148
BS02 ZN A C208 H250 C167 H209
BS03 GTV A H122 D124 H189 C208 N220 H81 D83 H148 C167 N179 MOAD: Ki=33.8uM
PDBbind-CN: -logKd/Ki=4.47,Ki=33.8uM
BindingDB: Ki=100000nM
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6d1d, PDBe:6d1d, PDBj:6d1d
PDBsum6d1d
PubMed31483651
UniProtC7C422|BLAN1_KLEPN Metallo-beta-lactamase type 2 (Gene Name=blaNDM-1)

[Back to BioLiP]