MolNFT v1 · #77616 · protein
Crystal structure of the chloride inhibited dihydrodipicolinate synthase from acinetobacter baumannii complexed with pyruvate at 1.8 a resolution
3RK8: “Crystal structure of the chloride inhibited dihydrodipicolinate synthase from acinetobacter baumannii…”. X-ray diffraction, 2 ligands (PYR, CL), 3 pockets (best druggability 0.78). MolNFT v1 #77616 on GenesisL1: 3D structure…
- PDB
- 3RK8
- 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
- PYR, CL
- Pockets
- 3 · 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 | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 291 | 49% helix, 13% strand | D0CFC3 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.78 | 0.86 | 64 | CL |
| 2 | 112 | 0.49 | 0.80 | 22 | PYR |
| 3 | 126 | 0.47 | 0.79 | 24 | PYR |
Interfaces
1 interface between chains.
- A–B · 1485 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3RK8 · Crystal structure of the chloride inhibited dihydrodipicolinate synthase from… · 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 3RK8 · PDBe 3RK8 · UniProt D0CFC3
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