Research workbench
Dihydrodipicolinate synthase with pyruvate from candidatus liberibacter solanacearum
Analyse Dihydrodipicolinate synthase with pyruvate from candidatus liberibacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LOY
- Type
- protein
- Length
- 1,770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- A0A0F4VK59
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 51% helix, 13% strand | A0A0F4VK59 |
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.74 | 0.84 | 50 | empty |
| 2 | 366 | 0.73 | 0.85 | 54 | empty |
| 3 | 432 | 0.70 | 0.81 | 62 | empty |
| 4 | 265 | 0.64 | 0.81 | 30 | empty |
| 5 | 259 | 0.63 | 0.82 | 35 | empty |
Interfaces
8 interfaces between chains.
- D–F · 1576 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1559 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 1554 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1010 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1003 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7LOY · Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum · the same entry in another collection · chain B against B, 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 A0A0F4VK59
- Elsewhere: RCSB PDB 7LOY · PDBe 7LOY · UniProt A0A0F4VK59
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