MolNFT v1 · #146516 · protein

Mtb clpb in complex with atpgammas and casein, conformer 1

6DJU · Chaperone protein clpb: “Mtb clpb in complex with atpgammas and casein, conformer 1”. Electron microscopy, 2 ligands (AGS, ADP), 20 pockets (best druggability 0.87). MolNFT v1 #146516 on GenesisL1: 3D structure, binding sites and…

PDB: 6DJU
Type: protein
Length: 3,502 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein clpb; Casein polyalanine model
UniProt: A0A045JSR5
Ligands: AGS, ADP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 7 distinct chains · 40% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein clpb	protein	610	44% helix, 9% strand	A0A045JSR5
B	Chaperone protein clpb	protein	611	41% helix, 10% strand	A0A045JSR5
C	Chaperone protein clpb	protein	614	42% helix, 10% strand	A0A045JSR5
D	Chaperone protein clpb	protein	562	38% helix, 9% strand	A0A045JSR5
N	Casein polyalanine model	protein	26	0% helix, 15% strand	—
E	Chaperone protein clpb	protein	548	39% helix, 7% strand	A0A045JSR5
F	Chaperone protein clpb	protein	531	39% helix, 8% strand	A0A045JSR5

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 10 copies · chains A, B, C, D, E, F
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F

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	920	0.87	0.89	134	ADP
2	1157	0.86	0.87	130	AGS
3	798	0.85	0.88	102	empty
4	1140	0.84	0.85	103	AGS
5	276	0.84	0.94	45	empty

Interfaces

14 interfaces between chains.

B–C · 4349 Å² buried · 57 hydrogen bonds · protein-protein
C–D · 4217 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 4076 Å² buried · 42 hydrogen bonds · protein-protein
D–E · 2202 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1728 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6DJU · Mtb ClpB in complex with ATPgammaS and casein, Conformer 1 · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A045JSR5
Elsewhere: RCSB PDB 6DJU · PDBe 6DJU · UniProt A0A045JSR5

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