Research workbench
Crystal structure of dihydrodipicolinate synthase from acinetobacter baumannii complexed with mg and cl ions at 1.80 a resolution
Analyse Crystal structure of dihydrodipicolinate synthase from acinetobacter baumannii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DXV
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- D0CFC3
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 291 | 50% helix, 13% strand | D0CFC3 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.75 | 0.84 | 50 | empty |
| 2 | 123 | 0.51 | 0.80 | 26 | CL |
| 3 | 120 | 0.50 | 0.80 | 28 | CL |
Interfaces
1 interface between chains.
- A–B · 1487 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4DXV · Crystal structure of Dihydrodipicolinate synthase from Acinetobacter baumannii complexed… · 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 D0CFC3
- Elsewhere: RCSB PDB 4DXV · PDBe 4DXV · UniProt D0CFC3
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