MolNFT v1 · #176363 · protein
Crystal structure of dsba-like protein DR2335 from deinococcus radiodurans R1, native protein
7DK9 · Dsba domain-containing protein: “Crystal structure of dsba-like protein DR2335 from deinococcus radiodurans R1, native protein”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.48). MolNFT v1 #176363 on GenesisL1…
- PDB
- 7DK9
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dsba domain-containing protein
- UniProt
- Q9RRZ4
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dsba domain-containing protein | protein | 212 | 53% helix, 11% strand | Q9RRZ4 |
| B | Dsba domain-containing protein | protein | 211 | 51% helix, 11% strand | Q9RRZ4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.48 | 0.77 | 25 | empty |
| 2 | 128 | 0.45 | 0.77 | 20 | empty |
| 3 | 92 | 0.40 | 0.78 | 17 | empty |
| 4 | 75 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1739 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7DK9 · Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native… · 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 Q9RRZ4
- Elsewhere: RCSB PDB 7DK9 · PDBe 7DK9 · UniProt Q9RRZ4
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