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Thermus thermophilus dnaj J- and G/F-domains

Analyse Thermus thermophilus dnaj J- and G/F-domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4J7Z
Type: protein
Length: 601 residues
Chains: 6
Method: x-ray diffraction; epr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnaj 2
UniProt: Q56237
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction; epr · 5 distinct chains · 55% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Chaperone protein dnaj 2	protein	100	55% helix, 0% strand	Q56237
C	Chaperone protein dnaj 2	protein	103	54% helix, 0% strand	Q56237
D	Chaperone protein dnaj 2	protein	106	54% helix, 0% strand	Q56237
E	Chaperone protein dnaj 2	protein	98	56% helix, 0% strand	Q56237
F	Chaperone protein dnaj 2	protein	94	56% helix, 0% strand	Q56237

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains B, C, E, F

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

Pockets

8 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	675	0.65	0.75	58	empty
2	98	0.62	0.88	20	empty
3	140	0.61	0.85	23	empty
4	241	0.57	0.79	27	GOL
5	161	0.48	0.77	24	empty

Interfaces

7 interfaces between chains.

C–D · 643 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 630 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 270 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 239 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 68 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4J7Z · Thermus thermophilus DNAJ J- and G/F-DOMAINS · the same entry in another collection · chain D against D, TM-score 1.00
Q56237 · AlphaFold monomer V2.0 prediction for chaperone protein dnaj 2 (Q56237) · a predicted model of the same protein · chain C 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 Q56237
Elsewhere: RCSB PDB 4J7Z · PDBe 4J7Z · UniProt Q56237

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