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Structural basis for the intermolecular communication between dnak and grpe in the dnak chaperone system from geobacillus kaustophilus HTA426

Analyse Structural basis for the intermolecular communication between dnak and grpe in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ANI
Type: protein
Length: 2,596 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein grpe; Chaperone protein dnak
UniProt: Q5KWZ6, Q5KWZ7
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein grpe	protein	156	55% helix, 15% strand	Q5KWZ6
B	Protein grpe	protein	154	51% helix, 19% strand	Q5KWZ6
C, D	Chaperone protein dnak	protein	509	35% helix, 30% strand	Q5KWZ7
E	Protein grpe	protein	135	56% helix, 9% strand	Q5KWZ6
F	Protein grpe	protein	130	47% helix, 6% strand	Q5KWZ6
G	Chaperone protein dnak	protein	502	30% helix, 25% strand	Q5KWZ7
H	Chaperone protein dnak	protein	501	30% helix, 26% strand	Q5KWZ7

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	1081	0.82	0.83	155	empty
2	1107	0.81	0.82	142	empty
3	803	0.80	0.83	107	empty
4	1125	0.75	0.78	122	empty
5	87	0.75	0.96	26	empty

Interfaces

20 interfaces between chains.

A–B · 1906 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1402 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 1388 Å² buried · 15 hydrogen bonds · protein-protein
D–G · 917 Å² buried · 15 hydrogen bonds · protein-protein
C–H · 906 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4ANI · Structural basis for the intermolecular communication between DnaK and GrpE in the DnaK… · the same entry in another collection · chain H against H, TM-score 1.00
Q5KWZ6 · AlphaFold monomer V2.0 prediction for protein grpe (Q5KWZ6) · a predicted model of the same protein · chain A against A, TM-score 0.73

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 Q5KWZ6
Every structure of UniProt Q5KWZ7
Elsewhere: RCSB PDB 4ANI · PDBe 4ANI · UniProt Q5KWZ6 · UniProt Q5KWZ7

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