MolNFT v1 · #149967 · protein

Cyanobacterial GAPDH with NAD

6GFR · Glyceraldehyde-3-phosphate dehydrogenase: “Cyanobacterial GAPDH with NAD”. X-ray diffraction, 2 ligands (NAD, MG), 3 pockets (best druggability 0.70). MolNFT v1 #149967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GFR
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.-
UniProt: Q8DIW5
Ligands: NAD, MG
Pockets: 3 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-)	protein	338	30% helix, 27% strand	Q8DIW5

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · chains A
ACT · Acetate ion · additive · 3 copies · chains A, B

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	746	0.70	0.77	82	NAD, ACT
2	461	0.65	0.78	45	NAD, ACT
3	370	0.55	0.74	44	empty

Interfaces

1 interface between chains.

A–B · 512 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6GFR · cyanobacterial GAPDH with NAD · 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 6GFR · PDBe 6GFR · UniProt Q8DIW5

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