MolNFT v1 · #28475 · protein
Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. COLI
1YFD · Ribonucleoside-diphosphate reductase 1 beta chain: “Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. COLI”. X-ray diffraction, 2 ligands (FEO, HG), 5 pockets (best druggability 0.74). MolNFT v1…
- 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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