Research workbench

Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase in complex with inhibitors

Analyse Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I32
Type: protein
Length: 2,148 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde 3-phosphate dehydrogenase
EC: 1.2.1.12
UniProt: Q27890
Ligands: NMD
Pockets: 7 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12)	protein	358	32% helix, 26% strand	Q27890

Ligands and binding sites

NMD · N-naphthalen-1-ylmethyl-2'-[3,5-dimethoxybenzamido]-2'-deoxy-adenosine · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	453	0.76	0.85	56	empty
2	1145	0.74	0.77	134	NMD
3	1146	0.74	0.77	136	NMD
4	483	0.74	0.83	54	empty
5	106	0.71	0.93	26	empty

Interfaces

7 interfaces between chains.

A–D · 2115 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 2093 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1439 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1424 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1398 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1I32 · Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase in complex with inhibitors · the same entry in another collection · chain F against F, TM-score 1.00
Q27890 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase… · 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 Q27890
Elsewhere: RCSB PDB 1I32 · PDBe 1I32 · UniProt Q27890

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.