Research workbench
Ribonucleotide reductase R2-D84E/W48F soaked with ferrous ions at pH 5
Analyse Ribonucleotide reductase R2-D84E/W48F soaked with ferrous ions at pH 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJ1
- 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 · 15 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 | 128 | 0.76 | 0.94 | 28 | empty |
| 2 | 62 | 0.55 | 0.88 | 19 | HG |
| 3 | 72 | 0.32 | 0.74 | 18 | empty |
| 4 | 62 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3043 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 1PJ1 · Ribonucleotide reductase R2-D84E/W48F soaked with ferrous ions at pH 5 · 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 P69924
- Elsewhere: RCSB PDB 1PJ1 · PDBe 1PJ1 · UniProt P69924
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