Structure of PDB 4g0d Chain B

Receptor sequence

>4g0dB (length=368) Species: 9606 (Homo sapiens) [Search protein sequence]

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHAFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPGDEDPNPKHPKTPDKCDPSLSLDAITSLRGETMIF
KDRFFWRLHPQQVDAELFLTKSFWPELPNRIDAAYEHPSHDLIFIFRGRK
FWALNGYDILEGYPKKISELGLPKEVKKISAAVHFEDTGKTLLFSGNQVW
RYDDTNHIMDKDYPRLIEEDFPGIGDKVDAVYEKNGYIYFFNGPIQFEYS
IWSNRIVRVMPANSILWC

3D structure

PDB

4g0d Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain.

Chain

Resolution

2.54 Å

3D
structure

Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Catalytic site (original residue number in PDB)	H222 A223 H226 H232
Catalytic site (residue number reindexed from 1)	H119 A120 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)
BS01	peptide	B	F107 L111 Y176 G183 L184 L185 A186 H187 A188 F189 P190 Y214 H222 H226 D231 H232 P242 I243 Y244	F4 L8 Y73 G80 L81 L82 A83 H84 A85 F86 P87 Y111 H119 H123 D128 H129 P139 I140 Y141
BS02	peptide	B	P331 R350 K353	P228 R247 K250
BS03	ZN	B	H222 H226 H232	H119 H123 H129
BS04	ZN	B	H172 D174 H187 H200	H69 D71 H84 H97
BS05	CA	B	D128 D203 E205	D25 D100 E102
BS06	CA	B	D179 G180 S182 L184 D202 E205	D76 G77 S79 L81 D99 E102
BS07	CA	B	D162 N194 G196 D198	D59 N91 G93 D95
BS08	CA	B	D291 D335 S383 D432	D188 D232 S280 D329
BS09	CA	B	I293 A337 A385 V434	I190 A234 A282 V331
BS10	CA	B	S146 T149 G269	S43 T46 G166

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:4g0d, PDBe:4g0d, PDBj:4g0d
PDBsum	4g0d
PubMed	23913860
UniProt	P45452\|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

[Back to BioLiP]