Research workbench
Oxidized ribonucleotide reductase R2-D84E mutant containing oxo- bridged diferric cluster
Analyse Oxidized ribonucleotide reductase R2-D84E mutant containing oxo- bridged… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PIU
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase 1 beta chain
- EC
- 1.17.4.1
- UniProt
- P69924
- Ligands
- HG, FE, O
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase 1 beta chain (EC 1.17.4.1) | protein | 340 | 69% helix, 4% strand | P69924 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 10 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- O · Oxygen atom · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.76 | 0.95 | 28 | empty |
| 2 | 98 | 0.48 | 0.80 | 20 | HG |
| 3 | 80 | 0.35 | 0.75 | 17 | empty |
| 4 | 86 | 0.35 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3050 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 1PIU · Oxidized ribonucleotide reductase R2-D84E mutant containing oxo-bridged diferric cluster · the same entry in another collection · chain A against A, TM-score 1.00
- P69924 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 1 subunit beta… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P69924
- Elsewhere: RCSB PDB 1PIU · PDBe 1PIU · UniProt P69924
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.