MolNFT v1 · #155727 · protein

Crystal structure of an oxido-reductase

6LGJ · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of an oxido-reductase”. X-ray diffraction, 1 ligand (NAD), 13 pockets (best druggability 0.83). MolNFT v1 #155727 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6LGJ
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, 2.6.99.-
UniProt: P16858
Ligands: NAD
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-)	protein	333	32% helix, 26% strand	P16858

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	910	0.83	0.85	108	empty
2	1012	0.77	0.79	114	NAD
3	555	0.71	0.79	60	NAD
4	494	0.68	0.79	62	NAD
5	54	0.37	0.80	12	empty

Interfaces

6 interfaces between chains.

C–D · 2054 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2040 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 1351 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1339 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 499 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6LGJ · Crystal structure of an oxido-reductase · the same entry in another collection · chain D against D, TM-score 1.00
P16858 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P16858) · a predicted model of the same protein · chain B 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 P16858
Elsewhere: RCSB PDB 6LGJ · PDBe 6LGJ · UniProt P16858

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