MolNFT v1 · #26395 · protein

Crystal structure of the CPN10 from thermus thermophilus HB8

1WNR · 10 kda chaperonin: “Crystal structure of the CPN10 from thermus thermophilus HB8”. X-ray diffraction, 6 pockets (best druggability 0.59). MolNFT v1 #26395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1WNR
Type: protein
Length: 545 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 10 kda chaperonin
UniProt: P61493
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F	10 kda chaperonin	protein	75	4% helix, 56% strand	P61493
C	10 kda chaperonin	protein	84	8% helix, 50% strand	P61493
G	10 kda chaperonin	protein	86	3% helix, 50% strand	P61493

Pockets

6 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	313	0.59	0.78	44	empty
2	328	0.57	0.76	45	empty
3	138	0.44	0.76	27	empty
4	152	0.43	0.75	27	empty
5	136	0.43	0.76	24	empty

Interfaces

7 interfaces between chains.

C–D · 873 Å² buried · 13 hydrogen bonds · protein-protein
A–G · 855 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 822 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 818 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 814 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1WNR · Crystal structure of the Cpn10 from Thermus thermophilus HB8 · the same entry in another collection · chain G against G, TM-score 1.00
P61493 · AlphaFold monomer V2.0 prediction for 10 kda chaperonin (P61493) · a predicted model of the same protein · chain F 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 P61493
Elsewhere: RCSB PDB 1WNR · PDBe 1WNR · UniProt P61493

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