Research workbench
Structure of the ribonucleotide reductase RNR2 homodimer from saccharomyces cerevisiae
Analyse Structure of the ribonucleotide reductase RNR2 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
- 1SMQ
- Type
- protein
- Length
- 1,294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase small chain 1
- EC
- 1.17.4.1
- UniProt
- P09938
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase small chain 1 (EC 1.17.4.1) | protein | 329 | 72% helix, 0% strand | P09938 |
| C, D | Ribonucleoside-diphosphate reductase small chain 1 (EC 1.17.4.1) | protein | 318 | 71% helix, 0% strand | P09938 |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.77 | 0.80 | 65 | empty |
| 2 | 898 | 0.77 | 0.80 | 62 | empty |
| 3 | 839 | 0.76 | 0.80 | 67 | empty |
| 4 | 814 | 0.75 | 0.79 | 61 | empty |
| 5 | 175 | 0.53 | 0.79 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–D · 1263 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1262 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1SMQ · Structure of the Ribonucleotide Reductase Rnr2 Homodimer from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P09938 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase small chain 1… · a predicted model of the same protein · chain C against A, TM-score 0.89
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 P09938
- Elsewhere: RCSB PDB 1SMQ · PDBe 1SMQ · UniProt P09938
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