MolNFT v1 · #152691 · protein

Crystal structure of GAPDH

6IQ6 · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of GAPDH”. X-ray diffraction, 1 ligand (AW9), 20 pockets (best druggability 0.76). MolNFT v1 #152691 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6IQ6
Type: protein
Length: 2,664 residues
Chains: 8
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: P04406
Ligands: AW9
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-)	protein	333	30% helix, 27% strand	P04406

Ligands and binding sites

AW9 · (2Z)-4-methoxy-4-oxobut-2-enoic acid · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	553	0.76	0.83	60	empty
2	1195	0.75	0.78	128	AW9
3	676	0.74	0.80	72	empty
4	592	0.74	0.81	60	empty
5	471	0.74	0.84	46	empty

Interfaces

16 interfaces between chains.

G–H · 2061 Å² buried · 33 hydrogen bonds · protein-protein
A–F · 2044 Å² buried · 31 hydrogen bonds · protein-protein
C–E · 2036 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 2020 Å² buried · 31 hydrogen bonds · protein-protein
A–H · 1452 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

6IQ6 · Crystal structure of GAPDH · the same entry in another collection · chain H against H, TM-score 1.00
P04406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P04406) · a predicted model of the same protein · chain F 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 P04406
Elsewhere: RCSB PDB 6IQ6 · PDBe 6IQ6 · UniProt P04406

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