Structure of PDB 4dz6 Chain F Binding Site BS01

Receptor Information

>4dz6 Chain F (length=168) Species: 139 (Borreliella burgdorferi)

SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKK
HYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATE
PKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFK
DNEILNYKRDDECEHYYC

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: 4dz6 Chain F Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dz6 Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): K13 Y53 H134 A135
• Binding residue (residue number reindexed from 1): K12 Y52 H133 A134
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K13 Y53 N131 H134 E145
• Catalytic site (residue number reindexed from 1): K12 Y52 N130 H133 E144
• 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:0016310 phosphorylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4dz6, PDBe:4dz6, PDBj:4dz6
• PDBsum: 4dz6
• PubMed: 29870023
• UniProt: O51419|NDK_BORBU Nucleoside diphosphate kinase (Gene Name=ndk)