Structure of PDB 8qka Chain A Binding Site BS02

Receptor Information

>8qka Chain A (length=228) Species: 573 (Klebsiella pneumoniae)

ATLFIADLHLQTEEPEITAGFLRFLQGEARQADALYILGDLFEAWIGDDD
PNPLHQQIASAIKAVVDAGVPCYFIHGNRDFLVGQRFARQSGMILLAEEE
RLDLYGREVLIMHGDTLCTDDQGYLAFRAKVHTPWIQRLFLALPLFIRHR
IAARMRIMDVNPQAVVDAMERHHVQWLIHGHTHRPAVHELQANGQPAWRV
VLGAWHSEGSMVKVTPDDVELIHFPFHH

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 8qka Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qka Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): D41 N79 H114 H195
• Binding residue (residue number reindexed from 1): D40 N78 H113 H181
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.1.54: UDP-2,3-diacylglucosamine diphosphatase.

Gene Ontology

Molecular Function

• GO:0008758 UDP-2,3-diacylglucosamine hydrolase activity
• GO:0016462 pyrophosphatase activity
• GO:0016787 hydrolase activity
• GO:0030145 manganese ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0009245 lipid A biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005886 plasma membrane
• GO:0019897 extrinsic component of plasma membrane

External links

• PDB: RCSB:8qka, PDBe:8qka, PDBj:8qka
• PDBsum: 8qka
• PubMed: 38579010
• UniProt: A6T5R0|LPXH_KLEP7 UDP-2,3-diacylglucosamine hydrolase (Gene Name=lpxH)