Structure of PDB 1vkm Chain D Binding Site BS02

Receptor Information

>1vkm Chain D (length=292) Species: 243274 (Thermotoga maritima MSB8)

KIHHHHHHVIIESRIEKGKPVVGMETTVFVHGLPRKEAIELFRRAKEISR
EKGFQLAVIGILKGKIVAGMSEEELEAMMREGADKVGTREIPIVVAEGKN
AATTVSATIFLSRRIGIEVVVTGGTGGVHPGRVDVSQDLTEMSSSRAVLV
SSGIKSILDVEATFEMLETLEIPLVGFRTNEFPLFFSRKSGRRVPRIENV
EEVLKIYESMKEMELEKTLMVLNPVPEEYEIPHDEIERLLEKIELEVEGK
EVTPFLLKKLVEMTNGRTLKANLALLEENVKLAGEIAVKLKR

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: 1vkm Chain F Residue 300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1vkm Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): E204 E206
• Binding residue (residue number reindexed from 1): E212 E214
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 4.2.1.70: pseudouridylate synthase.

Gene Ontology

Molecular Function

• GO:0004730 pseudouridylate synthase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016829 lyase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0001522 pseudouridine synthesis
• GO:0046113 nucleobase catabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1vkm, PDBe:1vkm, PDBj:1vkm
• PDBsum: 1vkm
• PubMed: 15822122
• UniProt: Q9X1H5|PSUG_THEMA Pseudouridine-5'-phosphate glycosidase (Gene Name=psuG)