MolNFT v1 · #34691 · protein
The crystal structure of D-amino acid amidase from ochrobactrum anthropi SV3 complexed with D-phenylalanine
2DNS: “The crystal structure of D-amino acid amidase from ochrobactrum anthropi SV3 complexed with D-phenylalanine”. X-ray diffraction, 2 ligands (DPN, BA), 20 pockets (best druggability 0.85). MolNFT v1 #34691 on GenesisL1: 3D structure…
- PDB
- 2DNS
- Type
- protein
- Length
- 2,088 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino acid amidase
- UniProt
- Q9LCC8
- Ligands
- DPN, BA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino acid amidase | protein | 362 | 35% helix, 20% strand | Q9LCC8 |
| C | D-amino acid amidase | protein | 360 | 34% helix, 21% strand | Q9LCC8 |
| D | D-amino acid amidase | protein | 355 | 35% helix, 21% strand | Q9LCC8 |
| E | D-amino acid amidase | protein | 349 | 35% helix, 19% strand | Q9LCC8 |
| F | D-amino acid amidase | protein | 300 | 37% helix, 17% strand | Q9LCC8 |
Ligands and binding sites
- DPN · D-phenylalanine · ligand · 5 copies · chains A, B, C, D, E
- BA · Barium ion · metal · 20 copies · chains A, D, F, B, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.85 | 0.86 | 117 | BA |
| 2 | 875 | 0.84 | 0.86 | 72 | BA |
| 3 | 774 | 0.76 | 0.80 | 104 | BA |
| 4 | 55 | 0.73 | 0.99 | 18 | DPN |
| 5 | 531 | 0.68 | 0.78 | 48 | empty |
Interfaces
9 interfaces between chains.
- A–B · 496 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 470 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 467 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 463 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 460 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 2DNS · 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 2DNS · PDBe 2DNS · UniProt Q9LCC8
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