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Crystal structure of an oxido-reductase with mutation and inhibitor

Analyse Crystal structure of an oxido-reductase with mutation and inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LGM
Type: protein
Length: 1,332 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase
EC: 1.2.1.12, 2.6.99.-
UniProt: P16858
Ligands: NAD, 9HB, PO4
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-)	protein	333	33% helix, 26% strand	P16858

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, B, D
9HB · Dimethyl fumarate · ligand · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	953	0.81	0.82	122	empty
2	672	0.70	0.78	61	NAD, PO4, 9HB
3	610	0.69	0.78	65	NAD, PO4, 9HB
4	622	0.69	0.78	57	PO4
5	613	0.69	0.78	57	NAD, PO4, 9HB

Interfaces

6 interfaces between chains.

B–C · 2030 Å² buried · 29 hydrogen bonds · protein-protein
A–D · 2029 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 1402 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1372 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 502 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6LGM · Crystal structure of an oxido-reductase with mutation and inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
P16858 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P16858) · a predicted model of the same protein · chain C 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 P16858
Elsewhere: RCSB PDB 6LGM · PDBe 6LGM · UniProt P16858

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