Structure of PDB 2d1n Chain B Binding Site BS04

Receptor Information

>2d1n Chain B (length=166) Species: 9606 (Homo sapiens)

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPG

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: 2d1n Chain B Residue 283

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2d1n Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453
• Resolution: 2.37 Å
• Binding residue (original residue number in PDB): D162 N194 G196 D198
• Binding residue (residue number reindexed from 1): D59 N91 G93 D95
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): H222 E223 H226 H232
• Catalytic site (residue number reindexed from 1): H119 E120 H123 H129
• Enzyme Commision number: 3.4.24.-

Gene Ontology

Molecular Function

• GO:0004222 metalloendopeptidase activity
• GO:0008237 metallopeptidase activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0031012 extracellular matrix

External links

• PDB: RCSB:2d1n, PDBe:2d1n, PDBj:2d1n
• PDBsum: 2d1n
• PubMed: 16603129
• UniProt: P45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)