Research workbench
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase
Analyse Crystal structure of glyceraldehyde-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
- 2YYY
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.59
- UniProt
- Q58546
- Ligands
- NAP
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.59) | protein | 342 | 38% helix, 25% strand | Q58546 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.64 | 0.77 | 47 | NAP |
| 2 | 481 | 0.63 | 0.77 | 50 | NAP |
| 3 | 51 | 0.52 | 0.88 | 12 | empty |
| 4 | 52 | 0.51 | 0.87 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1732 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2YYY · Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- Q58546 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (Q58546) · 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 Q58546
- Elsewhere: RCSB PDB 2YYY · PDBe 2YYY · UniProt Q58546
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