MolNFT v1 · #78412 · protein
Structure of yeast ribonucleotide reductase 1 with amppnp and cdp
3S8B · Ribonucleoside-diphosphate reductase large chain 1: “Structure of yeast ribonucleotide reductase 1 with amppnp and cdp”. X-ray diffraction, 3 ligands (CDP, ANP, MG), 5 pockets (best druggability 0.71). MolNFT v1 #78412 on GenesisL1…
- PDB
- 3S8B
- Type
- protein
- Length
- 659 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
- CDP, ANP, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large chain 1 (EC 1.17.4.1) | protein | 659 | 47% helix, 11% strand | P21524 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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
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 | 477 | 0.71 | 0.81 | 43 | CDP |
| 2 | 202 | 0.50 | 0.77 | 27 | empty |
| 3 | 185 | 0.45 | 0.75 | 25 | empty |
| 4 | 106 | 0.38 | 0.75 | 15 | ANP |
| 5 | 66 | 0.34 | 0.76 | 22 | empty |
Compared structures
- 3S8B · Structure of Yeast Ribonucleotide Reductase 1 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 3S8B · PDBe 3S8B · UniProt P21524
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