Structure of PDB 3dpf Chain B

Receptor sequence

>3dpfB (length=163) Species: 9606 (Homo sapiens)

MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFT
RISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAE
ETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSL
PQDDIDGIQAIYG

3D structure

• PDB: 3dpf Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S(1)' Subsite of Matrix Metalloproteinase 8 (MMP-8)
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H197 E198 H201 H207
• Catalytic site (residue number reindexed from 1): H118 E119 H122 H128
• Enzyme Commision number: 3.4.24.34: neutrophil collagenase.

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	CA	B	D137 G169 I170 G171 D173	D58 G90 I91 G92 D94
BS02	CA	B	D154 G155 N157 I159 D177 E180	D75 G76 N78 I80 D98 E101
BS03	ZN	B	H147 D149 H162 H175	H68 D70 H83 H96
BS04	ZN	B	H197 H201 H207	H118 H122 H128
BS05	AXB	B	I159 L160 A161 L193 H197 L214 Y216 P217 N218 Y219 A220 R222 Y227 S228 P230	I80 L81 A82 L114 H118 L135 Y137 P138 N139 Y140 A141 R143 Y148 S149 P151	BindingDB: IC50=57nM

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:3dpf, PDBe:3dpf, PDBj:3dpf
• PDBsum: 3dpf
• PubMed: 19173605
• UniProt: P22894|MMP8_HUMAN Neutrophil collagenase (Gene Name=MMP8)