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Crystal structure of human liver GAPDH

Analyse Crystal structure of human liver GAPDH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZNQ
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, liver
EC: 1.2.1.12
UniProt: P04406
Ligands: NAD
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O, P, R, Q	Glyceraldehyde-3-phosphate dehydrogenase, liver (EC 1.2.1.12)	protein	333	31% helix, 26% strand	P04406

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q

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

Pockets

12 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	1171	0.77	0.79	126	NAD
2	496	0.74	0.83	62	empty
3	642	0.73	0.80	70	empty
4	718	0.70	0.77	70	NAD
5	655	0.68	0.77	63	NAD

Interfaces

6 interfaces between chains.

O–P · 2053 Å² buried · 34 hydrogen bonds · protein-protein
R–Q · 2033 Å² buried · 26 hydrogen bonds · protein-protein
O–R · 1449 Å² buried · 21 hydrogen bonds · protein-protein
P–Q · 1448 Å² buried · 23 hydrogen bonds · protein-protein
O–Q · 470 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1ZNQ · Crystal Structure of Human Liver GAPDH · the same entry in another collection · chain Q against Q, TM-score 1.00
P04406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P04406) · a predicted model of the same protein · chain O 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 1ZNQ · PDBe 1ZNQ · UniProt P04406

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