Research workbench
Structure of yeast ribonucleotide reductase 1 R293A with amppnp and cdp
Analyse Structure of yeast ribonucleotide reductase 1 R293A with amppnp and cdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S8C
- Type
- protein
- Length
- 666 residues
- Chains
- 1
- 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
- Ligands
- ANP, CDP, MG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large chain 1 (EC 1.17.4.1) | protein | 666 | 45% helix, 11% strand | P21524 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- CDP · Cytidine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.67 | 0.81 | 42 | CDP |
| 2 | 356 | 0.61 | 0.78 | 36 | empty |
| 3 | 158 | 0.41 | 0.74 | 24 | empty |
| 4 | 98 | 0.39 | 0.76 | 15 | ANP |
| 5 | 65 | 0.33 | 0.76 | 22 | empty |
Compared structures
- 3S8C · Structure of Yeast Ribonucleotide Reductase 1 R293A with AMPPNP and CDP · 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 0.99
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 3S8C · PDBe 3S8C · UniProt P21524
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