Research workbench
Structure of the ribonucleotide reductase RNR4 homodimer from saccharomyces cerevisiae
Analyse Structure of the ribonucleotide reductase RNR4 homodimer from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SMS
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase small chain 2
- EC
- 1.17.4.1
- UniProt
- P49723
- Ligands
- HG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase small chain 2 (EC 1.17.4.1) | protein | 314 | 65% helix, 0% strand | P49723 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.76 | 0.87 | 36 | empty |
| 2 | 234 | 0.57 | 0.78 | 28 | HG |
| 3 | 231 | 0.56 | 0.78 | 28 | HG |
| 4 | 79 | 0.41 | 0.79 | 19 | empty |
| 5 | 71 | 0.41 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1306 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1SMS · Structure of the Ribonucleotide Reductase Rnr4 Homodimer from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P49723 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase small chain 2… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P49723
- Elsewhere: RCSB PDB 1SMS · PDBe 1SMS · UniProt P49723
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