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Crystal structure of the C-terminal domain of clpb

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

PDB: 4FCW
Type: protein
Length: 923 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein clpb
UniProt: Q9RA63
Ligands: ADP
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein clpb	protein	311	47% helix, 16% strand	Q9RA63
C, F	Chaperone protein clpb	protein	306	47% helix, 15% strand	Q9RA63

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, C, F

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1007	0.80	0.82	82	ADP
2	310	0.61	0.79	29	ADP
3	246	0.58	0.79	34	ADP
4	82	0.53	0.85	17	empty
5	62	0.47	0.84	19	empty

Interfaces

1 interface between chains.

A–C · 1182 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 modified (engineered).

Compared structures

4FCW · Crystal structure of the C-terminal domain of ClpB · the same entry in another collection · chain A against A, TM-score 1.00
Q9RA63 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (Q9RA63) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9RA63
Elsewhere: RCSB PDB 4FCW · PDBe 4FCW · UniProt Q9RA63

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