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Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from trypanosoma brucei determined from laue data

Analyse Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X0N
Type: protein
Length: 2,148 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
EC: 1.2.1.12
UniProt: P22512
Ligands: NAD, SO4
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, O, P, Q, R	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12)	protein	358	30% helix, 24% strand	P22512

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, O, P, Q, R
SO4 · Sulfate ion · ion · 12 copies · chains A, B, O, P, Q, R

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.83	0.84	112	empty
2	967	0.76	0.79	115	SO4, NAD
3	530	0.69	0.79	65	SO4, NAD
4	503	0.67	0.78	58	SO4, NAD
5	534	0.64	0.76	55	SO4, NAD

Interfaces

8 interfaces between chains.

A–B · 2020 Å² buried · 26 hydrogen bonds · protein-protein
Q–R · 2017 Å² buried · 23 hydrogen bonds · protein-protein
O–P · 2010 Å² buried · 22 hydrogen bonds · protein-protein
O–R · 1428 Å² buried · 23 hydrogen bonds · protein-protein
P–Q · 1425 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

2X0N · Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei… · the same entry in another collection · chain R against R, TM-score 1.00
P22512 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase… · a predicted model of the same protein · chain O against A, TM-score 0.98

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 P22512
Elsewhere: RCSB PDB 2X0N · PDBe 2X0N · UniProt P22512

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