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Structure of recombinant mouse collagenase-3 (mmp-13)

Analyse Structure of recombinant mouse collagenase-3 (mmp-13) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CXV
Type: protein
Length: 320 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (collagenase-3)
EC: 3.4.24.-
UniProt: P33435
Ligands: CBP, ZN, CA
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein (collagenase-3) (EC 3.4.24.-)	protein	160	25% helix, 19% strand	P33435

Ligands and binding sites

CBP · 2-{4-[4-(4-chloro-phenoxy)-benzenesulfonyl]-tetrahydro-pyran-4-yl}-N-hydroxy-acetamide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	325	0.63	0.79	41	ZN, CBP
2	338	0.61	0.78	47	ZN, CBP
3	112	0.39	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 760 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1CXV · Structure of recombinant mouse collagenase-3 (mmp-13) · the same entry in another collection · chain B against B, TM-score 1.00
P33435 · AlphaFold monomer V2.0 prediction for collagenase 3 (P33435) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P33435
Elsewhere: RCSB PDB 1CXV · PDBe 1CXV · UniProt P33435

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