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Crystal structure of stromelysin catalytic domain

Analyse Crystal structure of stromelysin catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QIC
Type: protein
Length: 644 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (stromelysin-1)
EC: 3.4.24.17
UniProt: P08254
Ligands: CA, ZN
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein (stromelysin-1) (EC 3.4.24.17)	protein	161	27% helix, 17% strand	P08254

Ligands and binding sites

CA · Calcium ion · metal · 12 copies · chains A, B, C, D
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	172	0.59	0.82	35	ZN
2	248	0.58	0.79	38	ZN
3	159	0.57	0.82	29	ZN
4	169	0.56	0.80	37	ZN
5	213	0.52	0.77	33	empty

Interfaces

2 interfaces between chains.

B–D · 307 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 43 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1QIC · Crystal structure of stromelysin catalytic domain · the same entry in another collection · chain A against A, TM-score 1.00
P08254 · AlphaFold monomer V2.0 prediction for stromelysin-1 (P08254) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P08254
Elsewhere: RCSB PDB 1QIC · PDBe 1QIC · UniProt P08254

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