Research workbench
Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa
Analyse Structural and biochemical characterization of diaminopimelate epimerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8QZY
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.69
- Source
- Pseudomonas aeruginosa PA14
- Molecule
- Diaminopimelate epimerase
- EC
- 5.1.1.7
- UniProt
- Q02E84
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · resolution 1.69 · 2 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 276 | 18% helix, 41% strand | Q02E84 |
| B | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 278 | 17% helix, 40% strand | Q02E84 |
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 | 324 | 0.59 | 0.77 | 38 | empty |
| 2 | 238 | 0.59 | 0.80 | 29 | empty |
| 3 | 112 | 0.43 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 767 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- Q02E84 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (Q02E84) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q02E84
- Elsewhere: RCSB PDB 8QZY · PDBe 8QZY · UniProt Q02E84
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