MolNFT v1 · #65121 · protein

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from burkholderia pseudomallei

3GNQ: “Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from burkholderia pseudomallei”. X-ray diffraction, 1 ligand (NAD), 19 pockets (best druggability 0.81). MolNFT v1 #65121 on GenesisL1: 3D structure, binding…

PDB: 3GNQ
Type: protein
Length: 2,679 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase, type I
EC: 1.2.1.-
UniProt: Q3JNL6
Ligands: NAD
Pockets: 19 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F, G, H	Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.-)	protein	335	30% helix, 28% strand	Q3JNL6
B	Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.-)	protein	334	30% helix, 28% strand	Q3JNL6

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 7 copies · chains A, B, C, D, E, F, G, H

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

Pockets

19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	908	0.81	0.83	109	empty
2	984	0.81	0.82	115	empty
3	747	0.76	0.81	84	NAD
4	829	0.72	0.77	67	NAD
5	726	0.72	0.78	73	NAD

Interfaces

14 interfaces between chains.

F–H · 2029 Å² buried · 41 hydrogen bonds · protein-protein
E–G · 2018 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 2017 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 2002 Å² buried · 36 hydrogen bonds · protein-protein
G–H · 1482 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3GNQ · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia… · 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 Q3JNL6
Elsewhere: RCSB PDB 3GNQ · PDBe 3GNQ · UniProt Q3JNL6

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