Research workbench
Crystal structure of D-tartrate dehydratase from bradyrhizobium japonicum complexed with mg++ and meso- tartrate
Analyse Crystal structure of D-tartrate dehydratase from bradyrhizobium japonicum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DW7
- Type
- protein
- Length
- 6,208 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLL6730 protein
- EC
- 4.2.1.81
- UniProt
- Q89FH0
- Ligands
- SRT, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | BLL6730 protein (EC 4.2.1.81) | protein | 388 | 38% helix, 19% strand | Q89FH0 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.85 | 0.87 | 108 | empty |
| 2 | 1041 | 0.85 | 0.86 | 122 | empty |
| 3 | 1011 | 0.84 | 0.85 | 98 | empty |
| 4 | 1128 | 0.84 | 0.85 | 112 | empty |
| 5 | 1054 | 0.79 | 0.81 | 82 | empty |
Interfaces
34 interfaces between chains.
- O–P · 1904 Ų buried · 29 hydrogen bonds · protein-protein
- M–N · 1889 Ų buried · 31 hydrogen bonds · protein-protein
- K–L · 1889 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1884 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1879 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2DW7 · Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with… · the same entry in another collection · chain P against P, 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 2DW7 · PDBe 2DW7 · UniProt Q89FH0
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