Research workbench
Low resolution crystal structure of human ribonucleotide reductase ALPHA6 hexamer in complex with datp
Analyse Low resolution crystal structure of human ribonucleotide reductase ALPHA6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D1Y
- 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
- Pockets
- 7 · best druggability 0.76
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 | 714 | 49% helix, 12% strand | P23921 |
| B | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 738 | 48% helix, 12% strand | P23921 |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.76 | 0.78 | 103 | empty |
| 2 | 995 | 0.75 | 0.78 | 95 | empty |
| 3 | 872 | 0.73 | 0.77 | 83 | empty |
| 4 | 647 | 0.70 | 0.78 | 65 | empty |
| 5 | 81 | 0.59 | 0.88 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1503 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5D1Y · Low resolution crystal structure of human ribonucleotide reductase alpha6 hexamer in… · 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 B against A, TM-score 0.98
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 5D1Y · PDBe 5D1Y · UniProt P23921
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