Structure of PDB 5ihe Chain B Binding Site BS04

Receptor Information

>5ihe Chain B (length=442) Species: 272844 (Pyrococcus abyssi GE5)

VVLDKYGYPILYYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPP
KVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGLV
NSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFKGFY
SKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKAF
LKFLEWLNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIPD
IFDQYEALANLLANVPEHITMFIGPGNHDAARPAIPQPEFYKEYAKPIYK
LKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGKPGLPMVELLKMR
HLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGVQLVNS
ATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 5ihe Chain B Residue 704

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ihe Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): E544 E550
• Binding residue (residue number reindexed from 1): E367 E373
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.1: exodeoxyribonuclease I.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0006260 DNA replication

External links

• PDB: RCSB:5ihe, PDBe:5ihe, PDBj:5ihe
• PDBsum: 5ihe
• PubMed: 27548043
• UniProt: Q9V2F3|DP2S_PYRAB DNA polymerase II small subunit (Gene Name=polB)