Structure of PDB 2d1n Chain A

Receptor sequence

>2d1nA (length=166) Species: 9606 (Homo sapiens)

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPG

3D structure

• 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
• Chain: A
• Resolution: 2.37 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	CA	A	D128 D203 E205	D25 D100 E102
BS06	FA4	A	Y176 L184 L185 A186 H222 E223 H226 H232 P236 A238 L239 F241 P242 I243 Y244 T245 F252	Y73 L81 L82 A83 H119 E120 H123 H129 P133 A135 L136 F138 P139 I140 Y141 T142 F149	MOAD: Ki=0.007uM PDBbind-CN: -logKd/Ki=8.15,Ki=7nM

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)