MolNFT v1 · #87044 · protein

Structure of GAPDH from thermosynechococcus elongatus

4BOY · Glyceraldehyde-3-phosphate dehydrogenase: “Structure of GAPDH from thermosynechococcus elongatus”. X-ray diffraction, 1 ligand (NAD), 4 pockets (best druggability 0.69). MolNFT v1 #87044 on GenesisL1: 3D structure, binding sites and…

PDB: 4BOY
Type: protein
Length: 676 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase
EC: 1.2.1.13
UniProt: Q8DIW5
Ligands: NAD
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.13)	protein	338	31% helix, 28% strand	Q8DIW5

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

4 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	733	0.69	0.76	72	NAD
2	542	0.66	0.77	60	NAD
3	345	0.54	0.74	42	empty
4	53	0.30	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 504 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4BOY · Structure of GAPDH from Thermosynechococcus elongatus · 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 Q8DIW5
Elsewhere: RCSB PDB 4BOY · PDBe 4BOY · UniProt Q8DIW5

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