MolNFT v1 · #80390 · protein

Human MMP13 in complex with L-glutamate motif inhibitor

3TVC · Collagenase 3: “Human MMP13 in complex with L-glutamate motif inhibitor”. X-ray diffraction, 3 ligands (E3P, CA, ZN), 2 pockets (best druggability 0.51). MolNFT v1 #80390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3TVC
Type: protein
Length: 169 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Collagenase 3
EC: 3.4.24.-
UniProt: P45452
Ligands: E3P, CA, ZN
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Collagenase 3 (EC 3.4.24.-)	protein	169	25% helix, 17% strand	P45452

Ligands and binding sites

E3P · N~2~-[3-(1,1':4',1''-terphenyl-4-yl)propanoyl]-L-alpha-glutamine · ligand · chains A
CA · Calcium ion · metal · 3 copies · chains A
ZN · Zinc ion · metal · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	148	0.51	0.79	27	ZN, E3P
2	72	0.38	0.78	16	empty

Compared structures

3TVC · Human MMP13 in complex with L-glutamate motif inhibitor · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P45452
Elsewhere: RCSB PDB 3TVC · PDBe 3TVC · UniProt P45452

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