MolNFT v1 · #66339 · protein
Crystal structure of human ribonucleotide reductase 1 bound to the effectors ttp and datp
3HNF · Ribonucleoside-diphosphate reductase large subunit: “Crystal structure of human ribonucleotide reductase 1 bound to the effectors ttp and datp”. X-ray diffraction, 4 ligands (TTP, DTP, MG), 10 pockets (best druggability 0.74).…
- PDB
- 3HNF
- Type
- protein
- Length
- 1,452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase large subunit
- EC
- 1.17.4.1
- UniProt
- P23921
- Ligands
- TTP, DTP, MG, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 715 | 48% helix, 10% strand | P23921 |
| B | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 737 | 47% helix, 12% strand | P23921 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.74 | 0.77 | 91 | TTP, SO4 |
| 2 | 775 | 0.73 | 0.78 | 83 | SO4 |
| 3 | 470 | 0.68 | 0.79 | 52 | empty |
| 4 | 473 | 0.67 | 0.79 | 53 | empty |
| 5 | 153 | 0.65 | 0.86 | 22 | MG, TTP |
Interfaces
1 interface between chains.
- A–B · 1322 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3HNF · Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and dATP · the same entry in another collection · chain A against A, TM-score 1.00
- P23921 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase large subunit… · 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 P23921
- Elsewhere: RCSB PDB 3HNF · PDBe 3HNF · UniProt P23921
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