Research workbench
Structure of eukaryotic rnr large subunit R1 complexed with designed ADP analog compound
Analyse Structure of eukaryotic rnr large subunit R1 complexed with designed ADP analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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