Structure of PDB 3hdi Chain B Binding Site BS03

Receptor Information

>3hdi Chain B (length=414) Species: 272558 (Halalkalibacterium halodurans C-125)

INTMTLDNGVRIITEKMSTVRSVSIGIWVGTGSRYESAEENGISHFLEHM
FFKGTNTRSAQEIAEFFDSIGGQVNAFTSKEYTCYYAKVLDDHAGQAIDT
LSDMFFHSTFQKEELEKERKVVFEEIKMVDDTPDDIVHDLLSSATYGKHS
LGYPILGTVETLNSFNEGMLRHYMDRFYTGDYVVISVAGNVHDELIDKIK
ETFSQVKPTTYNYQGEKPMFLPNRIVRKKETEQAHLCLGYPGLPIGDKDV
YALVLLNNVLGGSMSSRLFQDIREKRGLCYSVFSYHSSFRDSGMLTIYAG
TGHDQLDDLVYSIQETTSALAEKGLTEKELENGKEQLKGSLMLSLESTNS
RMSRNGKNELLLKKHRSLDEMIEQINAVQKQDVSRLAKILLSASPSISLI
NANGELPKALIHLE

Ligand information

• Ligand ID: CO
• InChI: InChI=1S/Co/q+2
• InChIKey: XLJKHNWPARRRJB-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Co+2]
  CACTVS 3.341: [Co++]
• Formula: Co
• Name: COBALT (II) ION
• DrugBank: DB14205
• PDB chain: 3hdi Chain B Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hdi Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): H46 H50 E126
• Binding residue (residue number reindexed from 1): H45 H49 E125
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): H46 E49 H50 E119 E126
• Catalytic site (residue number reindexed from 1): H45 E48 H49 E118 E125

Gene Ontology

Molecular Function

• GO:0004222 metalloendopeptidase activity
• GO:0008233 peptidase activity
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3hdi, PDBe:3hdi, PDBj:3hdi
• PDBsum: 3hdi
• PubMed: 19913481
• UniProt: Q9KA85