Research workbench
Crystal structure of human ribonucleotide reductase 1 bound to the effector ttp and substrate GDP
Analyse Crystal structure of human ribonucleotide reductase 1 bound to the effector ttp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HND
- Type
- protein
- Length
- 1,464 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, GDP, MG, SO4
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 729 | 46% helix, 11% strand | P23921 |
| B | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 735 | 46% helix, 12% strand | P23921 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.74 | 0.79 | 78 | GDP |
| 2 | 732 | 0.74 | 0.79 | 69 | GDP |
| 3 | 360 | 0.67 | 0.81 | 48 | empty |
| 4 | 281 | 0.63 | 0.81 | 34 | SO4 |
| 5 | 112 | 0.62 | 0.88 | 21 | TTP |
Interfaces
1 interface between chains.
- A–B · 1570 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3HND · Crystal structure of human ribonucleotide reductase 1 bound to the effector TTP and… · 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 3HND · PDBe 3HND · UniProt P23921
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