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Crystal structure of the theta class glutathione S-transferase from the citrus canker pathogen xanthomonas axonopodis pv. citri, apo form

Analyse Crystal structure of the theta class glutathione S-transferase from the citrus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NXV
Type: protein
Length: 760 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutathione S-transferase
UniProt: Q8PG02
Ligands: CL
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 60% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutathione S-transferase	protein	192	59% helix, 9% strand	Q8PG02
B	Glutathione S-transferase	protein	187	61% helix, 9% strand	Q8PG02
C	Glutathione S-transferase	protein	191	60% helix, 8% strand	Q8PG02
D	Glutathione S-transferase	protein	190	61% helix, 8% strand	Q8PG02

Ligands and binding sites

CL · Chloride ion · ion · 24 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 4 copies · chains B, C

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	451	0.68	0.79	51	CL
2	76	0.57	0.87	17	CL
3	191	0.52	0.78	30	CL
4	84	0.37	0.77	24	empty
5	58	0.32	0.76	16	empty

Interfaces

4 interfaces between chains.

C–D · 1139 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1097 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 353 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 279 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6NXV · Crystal structure of the theta class glutathione S-transferase from the citrus canker… · 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 Q8PG02
Elsewhere: RCSB PDB 6NXV · PDBe 6NXV · UniProt Q8PG02

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