Research workbench
Crystal structure of the complex of dhdps from acinetobacter baumannii with pyruvate at 1.4 a resolution
Analyse Crystal structure of the complex of dhdps from acinetobacter baumannii with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TAK
- 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
- Pockets
- 3 · best druggability 0.75
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
- GOL · Glycerol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.75 | 0.85 | 52 | empty |
| 2 | 107 | 0.47 | 0.80 | 24 | GOL, PYR |
| 3 | 104 | 0.46 | 0.80 | 23 | GOL |
Interfaces
1 interface between chains.
- A–B · 1482 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3TAK · Crystal structure of the complex of DHDPS from Acinetobacter baumannii with Pyruvate at… · 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 3TAK · PDBe 3TAK · UniProt D0CFC3
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