Research workbench
Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. COLI
Analyse Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YFD
- Type
- protein
- Length
- 681 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
- FEO, HG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase 1 beta chain (EC 1.17.4.1) | protein | 340 | 70% helix, 4% strand | P69924 |
| B | Ribonucleoside-diphosphate reductase 1 beta chain (EC 1.17.4.1) | protein | 341 | 68% helix, 4% strand | P69924 |
Ligands and binding sites
- FEO · Mu-oxo-diiron · ligand · 2 copies · chains A, B
- HG · Mercury (II) ion · metal · 13 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 | 133 | 0.74 | 0.93 | 26 | empty |
| 2 | 97 | 0.51 | 0.82 | 19 | HG |
| 3 | 58 | 0.47 | 0.85 | 16 | HG |
| 4 | 78 | 0.43 | 0.80 | 15 | empty |
| 5 | 56 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3109 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 1YFD · Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. 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 1YFD · PDBe 1YFD · UniProt P69924
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