MolNFT v1 · #33811 · protein
Structures of yeast ribonucleotide reductase I
2CVY · Ribonucleoside-diphosphate reductase large chain 1: “Structures of yeast ribonucleotide reductase I”. X-ray diffraction, 2 ligands (TTP, MG), 4 pockets (best druggability 0.57). MolNFT v1 #33811 on GenesisL1: 3D structure, binding…
- PDB
- 2CVY
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase large chain 1; 9-per peptide from…
- EC
- 1.17.4.1
- UniProt
- P21524, P09938
- Ligands
- TTP, MG
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large chain 1 (EC 1.17.4.1) | protein | 640 | 47% helix, 13% strand | P21524 |
| B | 9-per peptide from ribonucleoside-diphosphate reductase small chain 1 (EC 1.17.4.1) | protein | 7 | 0% helix, 0% strand | P09938 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.57 | 0.80 | 35 | empty |
| 2 | 218 | 0.53 | 0.77 | 34 | empty |
| 3 | 113 | 0.40 | 0.76 | 14 | TTP |
| 4 | 68 | 0.35 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2CVY · Structures of Yeast Ribonucleotide Reductase I · 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
- P09938 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase small chain 1… · a predicted model of the same protein · chain B against A, TM-score 0.45
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
- Every structure of UniProt P09938
- Elsewhere: RCSB PDB 2CVY · PDBe 2CVY · UniProt P21524 · UniProt P09938
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