MolNFT v1 · #20722 · protein
Autocatalytic generation of dopa in the engineered protein R2 F208Y from escherichia COLI ribonucleotide reductase and crystal structure of the dopa-208 protein
1RNR · Ribonucleotide reductase R1 protein: “Autocatalytic generation of dopa in the engineered protein R2 F208Y from escherichia COLI ribonucleotide…”. X-ray diffraction, 2 ligands (HG, FE), 5 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 1RNR
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase R1 protein
- EC
- 1.17.4.1
- UniProt
- P69924
- Ligands
- HG, FE
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleotide reductase R1 protein (EC 1.17.4.1) | protein | 340 | 70% helix, 4% strand | P69924 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 14 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.75 | 0.94 | 26 | empty |
| 2 | 57 | 0.56 | 0.89 | 18 | HG |
| 3 | 78 | 0.40 | 0.78 | 17 | empty |
| 4 | 72 | 0.33 | 0.75 | 15 | empty |
| 5 | 65 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3001 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1RNR · Autocatalytic generation of dopa in the engineered protein R2 F208Y from escherichia COLI… · 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 1RNR · PDBe 1RNR · UniProt P69924
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