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Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site
Analyse Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MJF
- Type
- protein
- Length
- 1,776 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Candidatus Liberibacter solanacearum
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- A0A0F4VK59
- Ligands
- E8U, ZGM
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 50% 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 | 50% helix, 13% strand | A0A0F4VK59 |
Ligands and binding sites
- E8U · (4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid · ligand · 6 copies · chains A, B, C, D, E, F
- ZGM · (4S)-4-hydroxy-2-oxoheptanedioic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.76 | 0.86 | 66 | empty |
| 2 | 468 | 0.72 | 0.82 | 71 | empty |
| 3 | 308 | 0.68 | 0.83 | 39 | empty |
| 4 | 289 | 0.65 | 0.81 | 36 | ZGM, E8U |
| 5 | 243 | 0.65 | 0.83 | 38 | E8U, ZGM |
Interfaces
8 interfaces between chains.
- D–F · 1547 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 1533 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1512 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 953 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 933 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 7MJF · Crystal structure of candidatus liberibacter solanacearum dihydrodipicolinate synthase… · 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 7MJF · PDBe 7MJF · UniProt A0A0F4VK59
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