Research workbench
Crystal structure of dihydrodipicolinate synthase (dhdps) from brucella suis 1330
Analyse Crystal structure of dihydrodipicolinate synthase (dhdps) from brucella suis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XGS
- Type
- protein
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q8G1R0
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 294 | 49% helix, 13% strand | Q8G1R0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.78 | 0.85 | 56 | empty |
| 2 | 518 | 0.78 | 0.85 | 51 | empty |
| 3 | 305 | 0.58 | 0.77 | 34 | CIT |
| 4 | 301 | 0.57 | 0.77 | 34 | CIT |
| 5 | 277 | 0.57 | 0.77 | 33 | CIT |
Interfaces
4 interfaces between chains.
- A–B · 1574 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1554 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 889 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 880 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XGS · Crystal Structure of Dihydrodipicolinate synthase (DHDPS) from Brucella suis 1330 · the same entry in another collection · chain D against D, TM-score 1.00
- Q8G1R0 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q8G1R0) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q8G1R0
- Elsewhere: RCSB PDB 6XGS · PDBe 6XGS · UniProt Q8G1R0
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