Research workbench
Crystal structure of the complex of dhydrodipicolinate synthase from acinetobacter baumannii with lysine at 2.3A resolution
Analyse Crystal structure of the complex of dhydrodipicolinate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PUL
- 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
- LYS, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 291 | 48% helix, 13% strand | D0CFC3 |
Ligands and binding sites
- LYS · Lysine · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.77 | 0.86 | 76 | SO4, GOL, ACT |
| 2 | 88 | 0.50 | 0.83 | 22 | LYS, ACT |
| 3 | 124 | 0.46 | 0.78 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1530 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3PUL · Crystal structure of the complex of Dhydrodipicolinate synthase from Acinetobacter… · 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 3PUL · PDBe 3PUL · UniProt D0CFC3
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