Research workbench
Ribonucleotide reductase R2 D84E mutant soaked with ferrous ions at neutral pH
Analyse Ribonucleotide reductase R2 D84E mutant soaked with ferrous ions at neutral pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PIZ
- 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
- 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 · 11 copies · chains A, B
- FE · Fe (III) ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.76 | 0.94 | 28 | empty |
| 2 | 91 | 0.51 | 0.83 | 19 | HG |
| 3 | 90 | 0.35 | 0.74 | 18 | empty |
| 4 | 64 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3057 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 1PIZ · Ribonucleotide reductase R2 D84E mutant soaked with ferrous ions at neutral pH · 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 1PIZ · PDBe 1PIZ · UniProt P69924
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