Research workbench
Crystal structure of dsba-like protein DR2335 from deinococcus radiodurans R1, C24S mutant protein
Analyse Crystal structure of dsba-like protein DR2335 from deinococcus radiodurans R1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DKA
- Type
- protein
- Length
- 421 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dsba domain-containing protein
- UniProt
- Q9RRZ4
- Pockets
- 9 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dsba domain-containing protein | protein | 211 | 54% helix, 9% strand | Q9RRZ4 |
| B | Dsba domain-containing protein | protein | 210 | 52% helix, 9% strand | Q9RRZ4 |
Ligands and binding sites
- ACT · Acetate ion · additive · 12 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.51 | 0.81 | 23 | ACT |
| 2 | 200 | 0.48 | 0.75 | 26 | empty |
| 3 | 176 | 0.47 | 0.75 | 20 | empty |
| 4 | 98 | 0.43 | 0.78 | 17 | empty |
| 5 | 92 | 0.40 | 0.78 | 20 | ACT |
Interfaces
1 interface between chains.
- A–B · 589 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 7DKA · Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, C24S… · 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 7DKA · PDBe 7DKA · UniProt Q9RRZ4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.