Research workbench
Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from leishmania mexicana: implications for structure-based drug design and a new position for the inorganic phosphate binding site
Analyse Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GYP
- Type
- protein
- Length
- 1,432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Leishmania mexicana
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- Q27890
- Ligands
- NAD, PO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.8 · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 358 | 30% helix, 27% strand | Q27890 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.76 | 0.85 | 60 | empty |
| 2 | 392 | 0.71 | 0.83 | 45 | empty |
| 3 | 571 | 0.71 | 0.80 | 60 | PO4, NAD |
| 4 | 559 | 0.71 | 0.80 | 58 | PO4, NAD |
| 5 | 563 | 0.70 | 0.79 | 57 | PO4, NAD |
Interfaces
6 interfaces between chains.
- A–D · 2111 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2108 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1474 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1472 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 561 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1GYP · Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from leishmania… · the same entry in another collection · chain D against D, 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 0.99
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 1GYP · PDBe 1GYP · UniProt Q27890
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