Research workbench
Peroxide bound oxidized rubrerythrin from pyrococcus furiosus
Analyse Peroxide bound oxidized rubrerythrin from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MPS
- 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
- FEO, PEO, FE
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, G, H, I, K | Rubrerythrin | protein | 170 | 67% helix, 6% strand | Q9UWP7 |
Ligands and binding sites
- FEO · Mu-oxo-diiron · ligand · 4 copies · chains A, B, D, I, F, K
- PEO · Hydrogen peroxide · ligand · chains F, K
- FE · Fe (III) ion · metal · 16 copies · chains A, B, D, I, F, K, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.72 | 0.76 | 83 | empty |
| 2 | 775 | 0.67 | 0.75 | 64 | empty |
| 3 | 227 | 0.47 | 0.73 | 20 | empty |
| 4 | 210 | 0.47 | 0.73 | 20 | empty |
| 5 | 195 | 0.46 | 0.74 | 23 | empty |
Interfaces
20 interfaces between chains.
- F–K · 4464 Ų buried · 68 hydrogen bonds · protein-protein
- D–I · 4406 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 4403 Ų buried · 63 hydrogen bonds · protein-protein
- G–H · 4394 Ų buried · 65 hydrogen bonds · protein-protein
- D–K · 493 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3MPS · Peroxide Bound Oxidized Rubrerythrin from Pyrococcus furiosus · 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 3MPS · PDBe 3MPS · UniProt Q9UWP7
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