Structure of PDB 4fvl Chain B

Receptor sequence

>4fvlB (length=368) Species: 9606 (Homo sapiens)

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHAFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPGDEDPNPKHPKTPDKCDPSLSLDAITSLRGETMIF
KDRFFWRLHPQQVDAELFLTKSFWPELPNRIDAAYEHPSHDLIFIFRGRK
FWALNGYDILEGYPKKISELGLPKEVKKISAAVHFEDTGKTLLFSGNQVW
RYDDTNHIMDKDYPRLIEEDFPGIGDKVDAVYEKNGYIYFFNGPIQFEYS
IWSNRIVRVMPANSILWC

3D structure

• PDB: 4fvl Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain.
• Chain: B
• Resolution: 2.436 Å

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)	Binding affinity
BS01	peptide	B	L111 Y176 S182 G183 L185 A186 H187 A188 F189 P190 Y214 H222 H226 D231 H232 P242 I243 Y244	L8 Y73 S79 G80 L82 A83 H84 A85 F86 P87 Y111 H119 H123 D128 H129 P139 I140 Y141
BS02	ZN	B	H222 H226 H232	H119 H123 H129
BS03	ZN	B	H172 D174 H187 H200	H69 D71 H84 H97
BS04	CA	B	D179 G180 S182 L184 D202 E205	D76 G77 S79 L81 D99 E102
BS05	CA	B	D162 N194 G196 D198	D59 N91 G93 D95
BS06	CA	B	D291 D335 S383 D432	D188 D232 S280 D329
BS07	CA	B	I293 A337 A385 V434	I190 A234 A282 V331
BS08	CA	B	D128 D203 E205	D25 D100 E102

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:4fvl, PDBe:4fvl, PDBj:4fvl
• PDBsum: 4fvl
• PubMed: 23913860
• UniProt: P45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)