MolNFT v1 · #34954 · protein
Crystal structure of the mutant K184A of D-tartrate dehydratase from bradyrhizobium japonicum complexed with mg++ and D-tartrate
2DW6 · BLL6730 protein: “Crystal structure of the mutant K184A of D-tartrate dehydratase from bradyrhizobium japonicum complexed with…”. X-ray diffraction, 1 ligand (MG), 13 pockets (best druggability 0.84). MolNFT v1 #34954 on GenesisL1…
- PDB
- 2DW6
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLL6730 protein
- EC
- 4.2.1.81
- UniProt
- Q89FH0
- Ligands
- MG
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | BLL6730 protein (EC 4.2.1.81) | protein | 388 | 40% helix, 18% strand | Q89FH0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- TAR · D(-)-tartaric acid · additive · 3 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.84 | 0.85 | 139 | empty |
| 2 | 230 | 0.66 | 0.84 | 42 | TLA |
| 3 | 188 | 0.57 | 0.81 | 36 | empty |
| 4 | 180 | 0.54 | 0.79 | 37 | empty |
| 5 | 145 | 0.51 | 0.79 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1902 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1827 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 377 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 289 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2DW6 · Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q89FH0 · AlphaFold monomer V2.0 prediction for D(-)-tartrate dehydratase (Q89FH0) · 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 Q89FH0
- Elsewhere: RCSB PDB 2DW6 · PDBe 2DW6 · UniProt Q89FH0
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