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Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor

Analyse Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XUC
Type: protein
Length: 335 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Collagenase 3
EC: 3.4.24.-
UniProt: P45452
Ligands: PB3, ZN, CA
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Collagenase 3 (EC 3.4.24.-)	protein	169	24% helix, 18% strand	P45452
B	Collagenase 3 (EC 3.4.24.-)	protein	166	23% helix, 18% strand	P45452

Ligands and binding sites

PB3 · N,N'-bis(3-methylbenzyl)pyrimidine-4,6-dicarboxamide · 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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	916	0.76	0.79	121	PB3

Interfaces

1 interface between chains.

A–B · 1222 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1XUC · Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P45452 · AlphaFold monomer V2.0 prediction for collagenase 3 (P45452) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 1XUC · PDBe 1XUC · UniProt P45452

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