MolNFT v1 · #52965 · protein
Human ribonucleotide reductase R1 subunit (RRM1) in complex with datp and mg.
2WGH · Ribonucleoside-diphosphate reductase large subunit: “Human ribonucleotide reductase R1 subunit (RRM1) in complex with datp and mg.”. X-ray diffraction, 2 ligands (DTP, MG), 10 pockets (best druggability 0.79). MolNFT v1 #52965 on…
- PDB
- 2WGH
- Type
- protein
- Length
- 1,301 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
- DTP, MG
- Pockets
- 10 · best druggability 0.79
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 | 644 | 48% helix, 12% strand | P23921 |
| B | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 657 | 48% helix, 12% strand | P23921 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.79 | 0.82 | 81 | GOL |
| 2 | 548 | 0.70 | 0.79 | 55 | empty |
| 3 | 162 | 0.69 | 0.89 | 24 | DTP |
| 4 | 437 | 0.69 | 0.80 | 47 | empty |
| 5 | 165 | 0.67 | 0.87 | 24 | DTP |
Interfaces
1 interface between chains.
- A–B · 1606 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2WGH · Human Ribonucleotide reductase R1 subunit (RRM1) in complex with dATP and Mg. · 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 2WGH · PDBe 2WGH · UniProt P23921
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