Research workbench
Human ribonucleotide reductase large subunit (alpha) with datp and cdp
Analyse Human ribonucleotide reductase large subunit (alpha) with datp and cdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AUI
- Type
- protein
- Length
- 4,470 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase large subunit
- EC
- 1.17.4.1
- UniProt
- P23921
- Ligands
- DTP, CDP, MG
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) | protein | 745 | 45% helix, 12% strand | P23921 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 12 copies · chains A, B, C, D, E, F
- CDP · Cytidine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.75 | 0.87 | 39 | DTP |
| 2 | 337 | 0.75 | 0.86 | 41 | DTP |
| 3 | 352 | 0.74 | 0.86 | 42 | DTP, MG |
| 4 | 373 | 0.74 | 0.85 | 46 | DTP, MG |
| 5 | 193 | 0.72 | 0.89 | 22 | DTP, MG |
Interfaces
6 interfaces between chains.
- C–D · 2144 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2138 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2135 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 930 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 917 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6AUI · Human ribonucleotide reductase large subunit (alpha) with dATP and CDP · the same entry in another collection · chain C against C, 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 0.98
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 6AUI · PDBe 6AUI · UniProt P23921
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