Research workbench
Crystal structure of leishmania mexicana glycerol-3- phosphate dehydrogenase complexed with dhap and NAD
Analyse Crystal structure of leishmania mexicana glycerol-3- phosphate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N1E
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate dehydrogenase
- EC
- 1.1.1.8
- UniProt
- P90551
- Ligands
- NDE
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerol-3-phosphate dehydrogenase (EC 1.1.1.8) | protein | 349 | 51% helix, 13% strand | P90551 |
Ligands and binding sites
- NDE · Adenosine 5'-(trihydrogen diphosphate) P'-5'-ester with 3-(aminocarbonyl)-4-(1-hydroxyl-2-oxo-3-phosphonooxy-propyl)-1-beta-D-ribofuranosylpyridinium inner salt · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.76 | 0.88 | 35 | empty |
| 2 | 234 | 0.75 | 0.89 | 37 | empty |
| 3 | 480 | 0.75 | 0.83 | 47 | NDE |
| 4 | 513 | 0.75 | 0.83 | 50 | NDE |
| 5 | 88 | 0.49 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2779 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 1N1E · Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P90551 · AlphaFold monomer V2.0 prediction for glycerol-3-phosphate dehydrogenase [NAD(+)]… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P90551
- Elsewhere: RCSB PDB 1N1E · PDBe 1N1E · UniProt P90551
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