Research workbench
Human ribonucleotide reductase R1 subunit (RRM1) in complex with datp and mg.
Analyse Human ribonucleotide reductase R1 subunit (RRM1) in complex with datp and mg. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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