MolNFT v1 · #109478 · protein
Crystal structure of human ribonucleotide reductase 1 bound to inhibitor
4X3V · Ribonucleoside-diphosphate reductase large subunit: “Crystal structure of human ribonucleotide reductase 1 bound to inhibitor”. X-ray diffraction, 2 ligands (TTP, 3X4), 9 pockets (best druggability 0.76). MolNFT v1 #109478 on…
- PDB
- 4X3V
- 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, 3X4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 714 | 45% helix, 10% strand | P23921 |
| B | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 738 | 41% helix, 10% strand | P23921 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- 3X4 · N~6~-{N-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)acetyl]-2-methyl-D-alanyl}-D-lysine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.76 | 0.78 | 91 | TTP |
| 2 | 636 | 0.73 | 0.80 | 76 | empty |
| 3 | 378 | 0.67 | 0.81 | 46 | empty |
| 4 | 331 | 0.65 | 0.80 | 43 | empty |
| 5 | 136 | 0.62 | 0.86 | 19 | TTP |
Interfaces
1 interface between chains.
- A–B · 1565 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4X3V · Crystal structure of human ribonucleotide reductase 1 bound to inhibitor · 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 4X3V · PDBe 4X3V · UniProt P23921
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