MolNFT v1 · #77903 · protein
Crystal structure of 5-nitp inhibition of yeast ribonucleotide reductase
3RSR · Ribonucleoside-diphosphate reductase large chain 1: “Crystal structure of 5-nitp inhibition of yeast ribonucleotide reductase”. X-ray diffraction, 2 ligands (N5P, MG), 6 pockets (best druggability 0.61). MolNFT v1 #77903 on…
- PDB
- 3RSR
- Type
- protein
- Length
- 610 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
- N5P, MG
- Pockets
- 6 · best druggability 0.61
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 | 610 | 47% helix, 13% strand | P21524 |
Ligands and binding sites
- N5P · 1-{2-deoxy-5-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro -1H-indole · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.61 | 0.82 | 42 | empty |
| 2 | 126 | 0.45 | 0.77 | 25 | empty |
| 3 | 79 | 0.38 | 0.77 | 23 | empty |
| 4 | 89 | 0.35 | 0.75 | 14 | empty |
| 5 | 53 | 0.28 | 0.74 | 11 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3RSR · Crystal Structure of 5-NITP Inhibition of Yeast Ribonucleotide Reductase · 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 1.00
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 3RSR · PDBe 3RSR · UniProt P21524
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