MolNFT v1 · #10146 · protein

GAPDH complexed with ADP-ribose

1IHY · Glyceraldehyde 3-phosphate dehydrogenase: “GAPDH complexed with ADP-ribose”. X-ray diffraction, 2 ligands (APR, SO4), 3 pockets (best druggability 0.80). MolNFT v1 #10146 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IHY
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
UniProt: P56649
Ligands: APR, SO4
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12)	protein	333	32% helix, 25% strand	P56649

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · 4 copies · chains A, C, B, D
SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	920	0.80	0.82	98	empty
2	1161	0.74	0.77	125	SO4, APR
3	1070	0.73	0.76	118	SO4, APR

Interfaces

6 interfaces between chains.

A–D · 2009 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 2003 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1333 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1316 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 561 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1IHY · GAPDH complexed with ADP-ribose · the same entry in another collection · chain C against C, TM-score 1.00
P56649 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P56649) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P56649
Elsewhere: RCSB PDB 1IHY · PDBe 1IHY · UniProt P56649

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