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Crystal structure of chaperonin-60 from paracoccus denitrificans

Analyse Crystal structure of chaperonin-60 from paracoccus denitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IOK
Type: protein
Length: 3,374 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperonin 60
UniProt: Q9Z462
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Chaperonin 60	protein	482	50% helix, 17% strand	Q9Z462

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1066	0.76	0.78	89	empty
2	1141	0.75	0.78	92	empty
3	1121	0.74	0.77	91	empty
4	1150	0.74	0.77	91	empty
5	677	0.68	0.77	52	empty

Interfaces

7 interfaces between chains.

C–D · 1297 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1294 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 1282 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1281 Å² buried · 10 hydrogen bonds · protein-protein
F–G · 1281 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1IOK · Crystal structure of chaperonin-60 from paracoccus denitrificans · the same entry in another collection · chain G against G, TM-score 1.00
Q9Z462 · AlphaFold monomer V2.0 prediction for 60 kda chaperonin (Q9Z462) · a predicted model of the same protein · chain G against A, TM-score 0.85

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 Q9Z462
Elsewhere: RCSB PDB 1IOK · PDBe 1IOK · UniProt Q9Z462

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