Research workbench
Dihydrodipicolinate synthase bound with allosteric inhibitor (S)- lysine from candidatus liberibacter solanacearum
Analyse Dihydrodipicolinate synthase bound with allosteric inhibitor (S)- lysine from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LVL
- Type
- protein
- Length
- 1,776 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
- Ligands
- LYS
- Pockets
- 16 · 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 | 296 | 51% helix, 13% strand | A0A0F4VK59 |
Ligands and binding sites
- LYS · Lysine · ligand · 6 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.74 | 0.85 | 53 | LYS |
| 2 | 671 | 0.74 | 0.80 | 81 | LYS |
| 3 | 396 | 0.73 | 0.84 | 66 | LYS |
| 4 | 303 | 0.67 | 0.82 | 43 | empty |
| 5 | 289 | 0.67 | 0.83 | 42 | empty |
Interfaces
8 interfaces between chains.
- C–E · 1548 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1547 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1534 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 978 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 945 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7LVL · Dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine from Candidatus… · 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 A0A0F4VK59
- Elsewhere: RCSB PDB 7LVL · PDBe 7LVL · UniProt A0A0F4VK59
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