Structure of PDB 3elm Chain A

Receptor sequence

>3elmA (length=164) Species: 9606 (Homo sapiens)

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYFMLPDDD
VQGIQSLYGPGDED

3D structure

• PDB: 3elm Discovery of potent, selective, and orally active carboxylic acid based inhibitors of matrix metalloproteinase-13
• Chain: A
• Resolution: 1.9 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	D128 D203 E205	D25 D100 E102
BS05	CA	A	D162 N194 Y195 G196 D198	D59 N91 Y92 G93 D95
BS06	CA	A	S146 T149	S43 T46
BS07	24F	A	Y176 L184 A186 H187 A188 V219 H222 E223 H226 H232 L239 F241 I243 Y244	Y73 L81 A83 H84 A85 V116 H119 E120 H123 H129 L136 F138 I140 Y141	MOAD: Ki=0.19nM PDBbind-CN: -logKd/Ki=9.72,Ki=0.19nM BindingDB: IC50=0.5nM,Ki=0.19nM

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:3elm, PDBe:3elm, PDBj:3elm
• PDBsum: 3elm
• PubMed: 19422229
• UniProt: P45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)