MolNFT v1 · #11560 · protein
Mn substituted ribonucleotide reductase R2 from E. COLI oxidized by hydrogen peroxide and hydroxylamine
1JQC · Protein R2 of ribonucleotide reductase: “Mn substituted ribonucleotide reductase R2 from E. COLI oxidized by hydrogen peroxide and hydroxylamine”. X-ray diffraction, 2 ligands (HG, MN), 4 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 1JQC
- 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, MN
- Pockets
- 4 · best druggability 0.73
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 | 71% 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 · 13 copies · chains A, B
- MN · Manganese (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 | 129 | 0.73 | 0.92 | 27 | empty |
| 2 | 80 | 0.48 | 0.82 | 15 | empty |
| 3 | 84 | 0.38 | 0.77 | 20 | empty |
| 4 | 51 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3038 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 1JQC · Mn substituted Ribonucleotide reductase R2 from E. Coli oxidized by hydrogen peroxide and… · 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 B 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 1JQC · PDBe 1JQC · UniProt P69924
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