Research workbench
Low resolution X-ray crystal structure of yeast RNR1P with datp bound in the a-site
Analyse Low resolution X-ray crystal structure of yeast RNR1P with datp bound in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PAW
- Type
- protein
- Length
- 2,956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase large chain 1
- EC
- 1.17.4.1
- UniProt
- P21524
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonucleoside-diphosphate reductase large chain 1 (EC 1.17.4.1) | protein | 739 | 21% helix, 6% strand | P21524 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.86 | 0.88 | 186 | empty |
| 2 | 961 | 0.86 | 0.88 | 158 | empty |
| 3 | 945 | 0.86 | 0.87 | 158 | empty |
| 4 | 1140 | 0.85 | 0.87 | 187 | empty |
| 5 | 567 | 0.80 | 0.87 | 114 | empty |
Interfaces
3 interfaces between chains.
- A–B · 512 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 480 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PAW · Low resolution X-ray crystal structure of Yeast Rnr1p with dATP bound in the A-site · the same entry in another collection · chain A against A, TM-score 1.00
- P21524 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase large chain 1… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P21524
- Elsewhere: RCSB PDB 3PAW · PDBe 3PAW · UniProt P21524
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