Research workbench
The crystal structure of a thioredoxin-like oxidoreductase from silicibacter pomeroyi dss-3
Analyse The crystal structure of a thioredoxin-like oxidoreductase from silicibacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GYK
- Type
- protein
- Length
- 693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 27KDA outer membrane protein
- UniProt
- Q5LKL9
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 27KDA outer membrane protein | protein | 174 | 55% helix, 14% strand | Q5LKL9 |
| B, C, D | 27KDA outer membrane protein | protein | 173 | 55% helix, 14% strand | Q5LKL9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.78 | 0.80 | 95 | EDO, SO4 |
| 2 | 1021 | 0.74 | 0.77 | 87 | empty |
| 3 | 75 | 0.37 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 511 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 363 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3GYK · The crystal structure of a thioredoxin-like oxidoreductase from Silicibacter pomeroyi… · 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 Q5LKL9
- Elsewhere: RCSB PDB 3GYK · PDBe 3GYK · UniProt Q5LKL9
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