MolNFT v1 · #68867 · protein
Structure of eukaryotic rnr large subunit R1 complexed with designed ADP analog compound
3K8T · Ribonucleoside-diphosphate reductase large chain 1: “Structure of eukaryotic rnr large subunit R1 complexed with designed ADP analog compound”. X-ray diffraction, 3 ligands (DGT, 2A5, MG), 6 pockets (best druggability 0.63). MolNFT…
- PDB
- 3K8T
- Type
- protein
- Length
- 640 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase large chain 1
- EC
- 1.17.4.1
- UniProt
- P21524
- Ligands
- DGT, 2A5, MG
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase large chain 1 (EC 1.17.4.1) | protein | 640 | 46% helix, 12% strand | P21524 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A
- 2A5 · 2'-deoxy-2'-(2-hydroxyethyl)adenosine 5'-(trihydrogen diphosphate) · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.63 | 0.79 | 44 | 2A5 |
| 2 | 208 | 0.54 | 0.78 | 36 | empty |
| 3 | 208 | 0.44 | 0.73 | 24 | empty |
| 4 | 100 | 0.39 | 0.76 | 15 | DGT |
| 5 | 73 | 0.36 | 0.77 | 23 | empty |
Compared structures
- 3K8T · Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound · the same entry in another collection · chain A against A, TM-score 1.00
- P21524 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase large chain 1… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P21524
- Elsewhere: RCSB PDB 3K8T · PDBe 3K8T · UniProt P21524
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