MolNFT v1 · #34307 · protein
Crystal structure of L-aspartate dehydrogenase from hyperthermophilic archaeon archaeoglobus fulgidus
2DC1: “Crystal structure of L-aspartate dehydrogenase from hyperthermophilic archaeon archaeoglobus fulgidus”. X-ray diffraction, 1 ligand (NAD), 7 pockets (best druggability 0.77). MolNFT v1 #34307 on GenesisL1: 3D structure, binding…
- PDB
- 2DC1
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-aspartate dehydrogenase
- EC
- 1.4.1.21
- UniProt
- O28440
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-aspartate dehydrogenase (EC 1.4.1.21) | protein | 236 | 39% helix, 32% strand | O28440 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.77 | 0.94 | 18 | empty |
| 2 | 326 | 0.74 | 0.85 | 43 | CIT, NAD |
| 3 | 358 | 0.71 | 0.83 | 43 | CIT, NAD |
| 4 | 200 | 0.50 | 0.76 | 49 | empty |
| 5 | 85 | 0.42 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2353 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 2DC1 · Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon… · the same entry in another collection · chain A against A, TM-score 1.00
- O28440 · AlphaFold monomer V2.0 prediction for L-aspartate dehydrogenase (O28440) · 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 O28440
- Elsewhere: RCSB PDB 2DC1 · PDBe 2DC1 · UniProt O28440
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