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X-ray crystal structure of glucose-6-phosphate 1-dehydrogenase from mycobacterium avium

Analyse X-ray crystal structure of glucose-6-phosphate 1-dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LGV
Type: protein
Length: 1,813 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose-6-phosphate 1-dehydrogenase
EC: 1.1.1.49
UniProt: A0QC59
Ligands: CL, SO4
Pockets: 16 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49)	protein	457	38% helix, 21% strand	A0QC59
B	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49)	protein	454	37% helix, 21% strand	A0QC59
D	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49)	protein	445	38% helix, 21% strand	A0QC59

Ligands and binding sites

CL · Chloride ion · ion · 5 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · chains B
GOL · Glycerol · additive · 2 copies · chains A
EDO · 1,2-ethanediol · additive · chains C

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

Pockets

16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1043	0.88	0.89	92	empty
2	800	0.75	0.80	60	empty
3	655	0.72	0.79	59	empty
4	741	0.72	0.78	57	empty
5	52	0.61	0.93	15	empty

Interfaces

6 interfaces between chains.

A–C · 2006 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1923 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 623 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 602 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 592 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4LGV · X-ray crystal structure of Glucose-6-phosphate 1-dehydrogenase from Mycobacterium avium · the same entry in another collection · chain D against D, 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 A0QC59
Elsewhere: RCSB PDB 4LGV · PDBe 4LGV · UniProt A0QC59

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