Structure of PDB 3q8y Chain D Binding Site BS02

Receptor Information

>3q8y Chain D (length=149)

MERTFLMIKPDAVQRNLIGEVISRIERKGLKLVGGKLMQVPMELAETHYG
EHQGKPFYNDLISFITSAPVFAMVVEGEDAVNVSRHIIGSTNPSEASPGS
IRGDLGLTVGRNIIHGSDSLESAEREINLWFNENEITSYASPRDAWLYE

Ligand information

• Ligand ID: VO4
• InChI: InChI=1S/4O.V/q;3*-1;
• InChIKey: LSGOVYNHVSXFFJ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341: [O-][V]([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-][V](=O)([O-])[O-]
• Formula: O4 V
• Name: VANADATE ION
• PDB chain: 3q8y Chain D Residue 159

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3q8y Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): K9 Y49 H115
• Binding residue (residue number reindexed from 1): K9 Y49 H115
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K9 Y49 N112 H115 E126
• Catalytic site (residue number reindexed from 1): K9 Y49 N112 H115 E126
• Enzyme Commision number: 2.7.4.6: nucleoside-diphosphate kinase.

Gene Ontology

Molecular Function

• GO:0004550 nucleoside diphosphate kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006183 GTP biosynthetic process
• GO:0006228 UTP biosynthetic process
• GO:0006241 CTP biosynthetic process
• GO:0009117 nucleotide metabolic process
• GO:0009142 nucleoside triphosphate biosynthetic process
• GO:0016310 phosphorylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3q8y, PDBe:3q8y, PDBj:3q8y
• PDBsum: 3q8y
• PubMed: 21745603
• UniProt: Q5HFV4|NDK_STAAC Nucleoside diphosphate kinase (Gene Name=ndk)