Research workbench
Crystal structure of D-erythronate-4-phosphate dehydrogenase complexed with NAD
Analyse Crystal structure of D-erythronate-4-phosphate dehydrogenase complexed with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O4C
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythronate-4-phosphate dehydrogenase
- EC
- 1.1.1.290
- UniProt
- Q9I3W9
- Ligands
- NAD, PO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Erythronate-4-phosphate dehydrogenase (EC 1.1.1.290) | protein | 380 | 42% helix, 16% strand | Q9I3W9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- TLA · L(+)-tartaric acid · additive · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.80 | 0.81 | 100 | GOL |
| 2 | 772 | 0.73 | 0.78 | 78 | PO4, NAD |
| 3 | 749 | 0.72 | 0.78 | 68 | NAD, TLA |
| 4 | 412 | 0.61 | 0.76 | 30 | empty |
| 5 | 54 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1163 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2O4C · Crystal Structure of D-Erythronate-4-phosphate Dehydrogenase Complexed with NAD · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I3W9 · AlphaFold monomer V2.0 prediction for erythronate-4-phosphate dehydrogenase (Q9I3W9) · 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 Q9I3W9
- Elsewhere: RCSB PDB 2O4C · PDBe 2O4C · UniProt Q9I3W9
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