Structure of PDB 5b5o Chain A

Receptor sequence

>5b5oA (length=167) Species: 9606 (Homo sapiens)

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGFMLPD
DDVQGIQSLYGPGDEDP

3D structure

• PDB: 5b5o Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (MMP)-13 Inhibitors with a 1,2,4-Triazol-3-yl Moiety as a Zinc Binding Group Using a Structure-Based Design Approach
• Chain: A
• Resolution: 1.2 Å

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.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	A	H222 H226 H232	H119 H123 H129
BS02	ZN	A	H172 D174 H187 H200	H69 D71 H84 H97
BS03	CA	A	D179 G180 S182 L184 D202 E205	D76 G77 S79 L81 D99 E102
BS04	CA	A	D162 N194 G196 D198	D59 N91 G93 D95
BS05	WMM	A	L218 H222 H232 L239 F241 P242 I243 Y244	L115 H119 H129 L136 F138 P139 I140 Y141	MOAD: ic50=1900nM PDBbind-CN: -logKd/Ki=5.72,IC50=1900nM

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:5b5o, PDBe:5b5o, PDBj:5b5o
• PDBsum: 5b5o
• PubMed: 27966948
• UniProt: P45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)