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Chaperone hscb from vibrio cholerae

Analyse Chaperone hscb from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IT5
Type: protein
Length: 665 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Co-chaperone protein hscb homolog
UniProt: Q9KTX9
Ligands: CA
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Co-chaperone protein hscb homolog	protein	164	79% helix, 0% strand	Q9KTX9
B, D	Co-chaperone protein hscb homolog	protein	169	74% helix, 0% strand	Q9KTX9
C	Co-chaperone protein hscb homolog	protein	163	80% helix, 0% strand	Q9KTX9

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A, B, C, D

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

Pockets

7 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	1123	0.77	0.79	91	CA
2	802	0.74	0.79	75	CA
3	703	0.73	0.79	73	empty
4	564	0.66	0.77	51	empty
5	315	0.64	0.80	30	empty

Interfaces

6 interfaces between chains.

B–D · 860 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 767 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 350 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 279 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 208 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 modified (engineered).

Compared structures

4IT5 · Chaperone HscB from Vibrio cholerae · the same entry in another collection · chain A against A, TM-score 1.00
Q9KTX9 · AlphaFold monomer V2.0 prediction for co-chaperone protein hscb homolog (Q9KTX9) · a predicted model of the same protein · chain C 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 Q9KTX9
Elsewhere: RCSB PDB 4IT5 · PDBe 4IT5 · UniProt Q9KTX9

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