Research workbench
Structure of dihydrodipicolinate synthase from the common grapevine
Analyse Structure of dihydrodipicolinate synthase from the common grapevine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TUU
- Type
- protein
- Length
- 2,456 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- D7U7T8
- Ligands
- BR, CL
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 307 | 48% helix, 14% strand | D7U7T8 |
Ligands and binding sites
- BR · Bromide ion · ion · 15 copies · chains A, B, C, D, H, E, F, G
- CL · Chloride ion · ion · 8 copies · chains A, B, C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.82 | 0.85 | 80 | empty |
| 2 | 707 | 0.82 | 0.86 | 80 | empty |
| 3 | 312 | 0.78 | 0.89 | 45 | empty |
| 4 | 319 | 0.77 | 0.89 | 41 | empty |
| 5 | 200 | 0.68 | 0.86 | 36 | empty |
Interfaces
13 interfaces between chains.
- B–C · 1854 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 1837 Ų buried · 18 hydrogen bonds · protein-protein
- E–H · 1835 Ų buried · 25 hydrogen bonds · protein-protein
- A–G · 1831 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 657 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 3TUU · Structure of dihydrodipicolinate synthase from the common grapevine · the same entry in another collection · 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 D7U7T8
- Elsewhere: RCSB PDB 3TUU · PDBe 3TUU · UniProt D7U7T8
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