Research workbench
Ribonucleoside-diphosphate reductase 1 beta chain
Analyse Ribonucleoside-diphosphate reductase 1 beta chain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XIK
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein R2 of ribonucleotide reductase
- EC
- 1.17.4.1
- UniProt
- P69924
- Ligands
- HG, FE2
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein R2 of ribonucleotide reductase (EC 1.17.4.1) | protein | 340 | 70% helix, 4% strand | P69924 |
| B | Protein R2 of ribonucleotide reductase (EC 1.17.4.1) | protein | 341 | 68% helix, 4% strand | P69924 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 10 copies · chains A, B
- FE2 · Fe (II) 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.72 | 0.93 | 27 | empty |
| 2 | 53 | 0.31 | 0.77 | 14 | empty |
| 3 | 64 | 0.31 | 0.74 | 18 | empty |
| 4 | 53 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3084 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 1XIK · Ribonucleoside-diphosphate reductase 1 beta chain · 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 1XIK · PDBe 1XIK · UniProt P69924
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