MolNFT v1 · #1627 · protein

Glyceraldehyde 3-phosphate dehydrogenase

1B7G · Protein (glyceraldehyde 3-phosphate dehydrogenase): “Glyceraldehyde 3-phosphate dehydrogenase”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.65). MolNFT v1 #1627 on GenesisL1: 3D structure, binding sites and…

PDB: 1B7G
Type: protein
Length: 680 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (glyceraldehyde 3-phosphate dehydrogenase)
EC: 1.2.1.12
UniProt: P39460
Ligands: SO4
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O, Q	Protein (glyceraldehyde 3-phosphate dehydrogenase) (EC 1.2.1.12)	protein	340	36% helix, 24% strand	P39460

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains O, Q

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

Pockets

7 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	465	0.65	0.78	50	SO4
2	509	0.64	0.76	52	SO4
3	484	0.63	0.76	38	empty
4	101	0.63	0.88	18	empty
5	102	0.57	0.85	17	empty

Interfaces

1 interface between chains.

O–Q · 1744 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1B7G · Glyceraldehyde 3-phosphate dehydrogenase · the same entry in another collection · chain O against O, TM-score 1.00
P39460 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P39460) · 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 P39460
Elsewhere: RCSB PDB 1B7G · PDBe 1B7G · UniProt P39460

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