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The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine amide
Analyse The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EFX
- Type
- protein
- Length
- 2,073 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Ochrobactrum anthropi
- Molecule
- D-amino acid amidase
- UniProt
- Q9LCC8
- Ligands
- NFA, BA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.2 · 5 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino acid amidase | protein | 362 | 35% helix, 22% strand | Q9LCC8 |
| C | D-amino acid amidase | protein | 358 | 34% helix, 22% strand | Q9LCC8 |
| D | D-amino acid amidase | protein | 350 | 37% helix, 21% strand | Q9LCC8 |
| E | D-amino acid amidase | protein | 345 | 37% helix, 20% strand | Q9LCC8 |
| F | D-amino acid amidase | protein | 296 | 34% helix, 13% strand | Q9LCC8 |
Ligands and binding sites
- NFA · Phenylalanine amide · ligand · 6 copies · chains A, B, C, D, E, F
- BA · Barium ion · metal · 22 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.85 | 0.88 | 87 | BA |
| 2 | 769 | 0.84 | 0.87 | 71 | BA |
| 3 | 332 | 0.74 | 0.86 | 46 | empty |
| 4 | 216 | 0.74 | 0.89 | 31 | NFA |
| 5 | 302 | 0.70 | 0.84 | 46 | NFA |
Interfaces
9 interfaces between chains.
- D–E · 548 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 539 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 494 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 478 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2EFX · The crystal structure of D-amino acid amidase from ochrobactrum anthropi SV3 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 Q9LCC8
- Elsewhere: RCSB PDB 2EFX · PDBe 2EFX · UniProt Q9LCC8
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