MolNFT v1 · #66336 · protein
Crystal structure of human ribonucleotide reductase 1 bound to the effector ttp
3HNC · Ribonucleoside-diphosphate reductase large subunit: “Crystal structure of human ribonucleotide reductase 1 bound to the effector ttp”. X-ray diffraction, 3 ligands (TTP, MG, SO4), 10 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 3HNC
- 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, MG, SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 714 | 49% helix, 12% strand | P23921 |
| B | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 738 | 48% helix, 12% strand | P23921 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.75 | 0.78 | 97 | TTP, SO4 |
| 2 | 730 | 0.71 | 0.77 | 78 | SO4 |
| 3 | 472 | 0.68 | 0.79 | 49 | empty |
| 4 | 541 | 0.66 | 0.77 | 60 | empty |
| 5 | 122 | 0.63 | 0.88 | 21 | MG, TTP |
Interfaces
1 interface between chains.
- A–B · 1413 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3HNC · Crystal structure of human ribonucleotide reductase 1 bound to the effector TTP · 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 3HNC · PDBe 3HNC · UniProt P23921
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