Research workbench

MMP-13 in complex with the peptide IMISF

Analyse MMP-13 in complex with the peptide IMISF in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HV2
Type: protein
Length: 171 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.709
Source: Homo sapiens
Molecule: Collagenase 3
EC: 3.4.24.-
UniProt: P45452
Ligands: CA, ZN
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · resolution 1.709 · 2 distinct chains · 23% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Collagenase 3 (EC 3.4.24.-)	protein	166	23% helix, 19% strand	P45452
B	Collagenase 3 (EC 3.4.24.-)	protein	5	0% helix, 40% strand	P45452

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A
ZN · Zinc ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	73	0.47	0.83	18	empty
2	57	0.32	0.76	17	empty
3	63	0.30	0.74	13	GOL

Interfaces

1 interface between chains.

A–B · 446 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6HV2 · Mmp-13 in complex with the peptide imisf · 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 A against A, TM-score 0.97

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 6HV2 · PDBe 6HV2 · UniProt P45452

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