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The crystal structure of D-amino acid amidase from ochrobactrum anthropi SV3 complexed with L-phenylalanine
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
- 2EFU
- Type
- protein
- Length
- 2,104 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino acid amidase
- UniProt
- Q9LCC8
- Ligands
- PHE, BA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-amino acid amidase | protein | 362 | 34% helix, 21% strand | Q9LCC8 |
| B | D-amino acid amidase | protein | 359 | 35% helix, 20% strand | Q9LCC8 |
| C | D-amino acid amidase | protein | 361 | 36% helix, 21% strand | Q9LCC8 |
| D | D-amino acid amidase | protein | 350 | 36% helix, 21% strand | Q9LCC8 |
| E | D-amino acid amidase | protein | 342 | 37% helix, 20% strand | Q9LCC8 |
| F | D-amino acid amidase | protein | 330 | 36% helix, 20% strand | Q9LCC8 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 6 copies · chains A, B, C, D, E, F
- BA · Barium ion · metal · 25 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.84 | 0.86 | 95 | BA |
| 2 | 926 | 0.84 | 0.86 | 78 | BA |
| 3 | 901 | 0.74 | 0.78 | 92 | empty |
| 4 | 327 | 0.73 | 0.85 | 46 | BA, PHE |
| 5 | 71 | 0.73 | 0.97 | 22 | PHE |
Interfaces
9 interfaces between chains.
- D–E · 551 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 520 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 495 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 472 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 467 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2EFU · The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed… · the same entry in another collection · chain B against B, 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 2EFU · PDBe 2EFU · UniProt Q9LCC8
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