Research workbench
D-threo-3-hydroxyaspartate dehydratase from delftia sp. HT23 complexed with D-erythro-3-hydroxyaspartate
Analyse D-threo-3-hydroxyaspartate dehydratase from delftia sp. HT23 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WQD
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-threo-3-hydroxyaspartate dehydratase
- EC
- 4.3.1.27
- UniProt
- B2DFG5
- Ligands
- PLP, 999, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-threo-3-hydroxyaspartate dehydratase (EC 4.3.1.27) | protein | 379 | 37% helix, 25% strand | B2DFG5 |
| B | D-threo-3-hydroxyaspartate dehydratase (EC 4.3.1.27) | protein | 389 | 40% helix, 24% strand | B2DFG5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 999 · (3S)-3-hydroxy-D-aspartic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.80 | 0.83 | 100 | PLP, MG, 999 |
| 2 | 98 | 0.40 | 0.77 | 16 | empty |
| 3 | 72 | 0.36 | 0.77 | 15 | MG |
| 4 | 78 | 0.32 | 0.74 | 15 | empty |
| 5 | 65 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2427 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3WQD · D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- B2DFG5 · AlphaFold monomer V2.0 prediction for D-threo-3-hydroxyaspartate dehydratase (B2DFG5) · 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 B2DFG5
- Elsewhere: RCSB PDB 3WQD · PDBe 3WQD · UniProt B2DFG5
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