MolNFT v1 · #33810 · protein
Structures of yeast ribonucleotide reductase I
2CVX · Ribonucleoside-diphosphate reductase large chain 1: “Structures of yeast ribonucleotide reductase I”. X-ray diffraction, 3 ligands (DGT, ADP, MG), 4 pockets (best druggability 0.72). MolNFT v1 #33810 on GenesisL1: 3D structure…
- PDB
- 2CVX
- Type
- protein
- Length
- 664 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
- DGT, ADP, MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large chain 1 (EC 1.17.4.1) | protein | 664 | 47% helix, 13% strand | P21524 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A
- ADP · Adenosine-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
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 | 548 | 0.72 | 0.81 | 63 | ADP |
| 2 | 317 | 0.55 | 0.75 | 25 | empty |
| 3 | 114 | 0.41 | 0.76 | 14 | DGT |
| 4 | 74 | 0.34 | 0.76 | 21 | empty |
Compared structures
- 2CVX · 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
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 2CVX · PDBe 2CVX · UniProt P21524
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