MolNFT v1 · #91424 · protein

Crystal structure of the C-terminal domain of clpb

4FCV · Chaperone protein clpb: “Crystal structure of the C-terminal domain of clpb”. X-ray diffraction, 1 ligand (ADP), 7 pockets (best druggability 0.80). MolNFT v1 #91424 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FCV
Type: protein
Length: 933 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 · 1 distinct chain · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Chaperone protein clpb	protein	311	48% helix, 16% strand	Q9RA63

Ligands and binding sites

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

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	918	0.80	0.82	79	ADP
2	853	0.80	0.83	78	ADP
3	179	0.61	0.83	20	empty
4	285	0.57	0.77	26	ADP
5	155	0.50	0.79	20	empty

Interfaces

2 interfaces between chains.

B–C · 1318 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1103 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 modified (engineered).

Compared structures

4FCV · 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 B 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 4FCV · PDBe 4FCV · UniProt Q9RA63

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