MolNFT v1 · #34815 · protein
The crystal structutre of D-amino acid amidase from ochrobactrum anthropi SV3
2DRW: “The crystal structutre of D-amino acid amidase from ochrobactrum anthropi SV3”. X-ray diffraction, 1 ligand (BA), 20 pockets (best druggability 0.85). MolNFT v1 #34815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DRW
- 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
- BA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino acid amidase | protein | 362 | 35% helix, 21% strand | Q9LCC8 |
| C | D-amino acid amidase | protein | 358 | 35% helix, 21% strand | Q9LCC8 |
| D | D-amino acid amidase | protein | 350 | 36% helix, 21% strand | Q9LCC8 |
| E | D-amino acid amidase | protein | 345 | 36% helix, 21% strand | Q9LCC8 |
| F | D-amino acid amidase | protein | 327 | 36% helix, 19% strand | Q9LCC8 |
Ligands and binding sites
- BA · Barium ion · metal · 23 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.85 | 0.86 | 99 | BA |
| 2 | 1198 | 0.84 | 0.85 | 116 | BA |
| 3 | 842 | 0.76 | 0.80 | 111 | BA |
| 4 | 79 | 0.74 | 0.97 | 23 | empty |
| 5 | 346 | 0.70 | 0.83 | 48 | empty |
Interfaces
9 interfaces between chains.
- D–E · 537 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 505 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 495 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 481 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 481 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2DRW · The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3 · 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 2DRW · PDBe 2DRW · UniProt Q9LCC8
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