Research workbench
Exposure of rubrerythrin from pyrococcus furiosus to peroxide, fifteen second time point.
Analyse Exposure of rubrerythrin from pyrococcus furiosus to peroxide, fifteen second… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QVD
- Type
- protein
- Length
- 1,360 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubrerythrin
- UniProt
- Q9UWP7
- Ligands
- PEO, FE2, FE
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Rubrerythrin | protein | 170 | 68% helix, 6% strand | Q9UWP7 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- FE2 · Fe (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.69 | 0.77 | 75 | empty |
| 2 | 708 | 0.69 | 0.77 | 72 | empty |
| 3 | 171 | 0.47 | 0.76 | 23 | empty |
| 4 | 164 | 0.45 | 0.75 | 25 | empty |
| 5 | 194 | 0.45 | 0.73 | 19 | empty |
Interfaces
20 interfaces between chains.
- G–H · 4379 Ų buried · 56 hydrogen bonds · protein-protein
- E–F · 4364 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 4358 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 4351 Ų buried · 57 hydrogen bonds · protein-protein
- A–G · 482 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3QVD · Exposure of rubrerythrin from Pyrococcus furiosus to peroxide, fifteen second time point. · 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 Q9UWP7
- Elsewhere: RCSB PDB 3QVD · PDBe 3QVD · UniProt Q9UWP7
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