Research workbench
Crystal structure of dihydrodipicolinate synthase from staphylococcus aureus
Analyse Crystal structure of dihydrodipicolinate synthase from staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DI0
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q5HG25
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 291 | 47% helix, 14% strand | Q5HG25 |
| B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 292 | 48% helix, 13% strand | Q5HG25 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.78 | 0.85 | 68 | GOL |
| 2 | 243 | 0.59 | 0.80 | 25 | empty |
| 3 | 221 | 0.58 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1762 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3DI0 · Crystal Structure of Dihydrodipicolinate synthase from Staphylococcus aureus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HG25 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q5HG25) · a predicted model of the same protein · chain A 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 Q5HG25
- Elsewhere: RCSB PDB 3DI0 · PDBe 3DI0 · UniProt Q5HG25
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