MolNFT v1 · #19819 · protein

Crystal structure analysis of clpb

1QVR · Clpb protein: “Crystal structure analysis of clpb”. X-ray diffraction, 2 ligands (ANP, PT), 20 pockets (best druggability 0.87). MolNFT v1 #19819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1QVR
Type: protein
Length: 2,409 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clpb protein
UniProt: Q9RA63
Ligands: ANP, PT
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Clpb protein	protein	803	57% helix, 9% strand	Q9RA63

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C
PT · Platinum (II) ion · metal · 23 copies · chains B, C, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	871	0.87	0.89	87	ANP
2	266	0.84	0.95	33	empty
3	933	0.84	0.85	84	ANP
4	1005	0.81	0.83	71	ANP
5	373	0.70	0.82	46	empty

Interfaces

2 interfaces between chains.

B–C · 2672 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2002 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

1QVR · Crystal Structure Analysis 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 0.81

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 1QVR · PDBe 1QVR · UniProt Q9RA63

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