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Crystal structure of thioacylenzyme intermediate of an NADP dependent aldehyde dehydrogenase
Analyse Crystal structure of thioacylenzyme intermediate of an NADP dependent aldehyde… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ESD
- Type
- protein
- Length
- 1,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.9
- UniProt
- Q59931
- Ligands
- NAP, G3H
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 474 | 43% helix, 23% strand | Q59931 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- G3H · Glyceraldehyde-3-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.84 | 0.88 | 80 | empty |
| 2 | 767 | 0.83 | 0.86 | 83 | empty |
| 3 | 454 | 0.76 | 0.85 | 44 | empty |
| 4 | 499 | 0.68 | 0.79 | 53 | NAP, G3H |
| 5 | 500 | 0.68 | 0.78 | 46 | NAP |
Interfaces
6 interfaces between chains.
- A–B · 2593 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2580 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1203 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1149 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 835 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2ESD · Crystal Structure of thioacylenzyme intermediate of an Nadp Dependent Aldehyde… · the same entry in another collection · chain D against D, TM-score 1.00
- Q59931 · AlphaFold monomer V2.0 prediction for NADP-dependent glyceraldehyde-3-phosphate… · a predicted model of the same protein · chain A 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 Q59931
- Elsewhere: RCSB PDB 2ESD · PDBe 2ESD · UniProt Q59931
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