MolNFT v2 · #115858 · protein
Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to CDP and dATP at 2.97 Angstroms resolution
5CNS · Ribonucleoside-diphosphate reductase 1 subunit alpha: “Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to CDP and…”. X-ray diffraction at 2.975, 5 ligands (CDP, DAT, DTP), 20 pockets…
- PDB
- 5CNS
- Type
- protein
- Length
- 4,353 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.975
- Source
- Escherichia coli (strain K12)
- Molecule
- Ribonucleoside-diphosphate reductase 1 subunit alpha; Ribonucleoside-diphosphate…
- EC
- 1.17.4.1
- UniProt
- P00452, P69924
- Ligands
- CDP, DAT, DTP, FEO, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.975 · 5 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 732 | 45% helix, 13% strand | P00452 |
| B, D | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 734 | 46% helix, 13% strand | P00452 |
| E | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 352 | 67% helix, 4% strand | P69924 |
| F, G | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 357 | 68% helix, 4% strand | P69924 |
| H | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 355 | 68% helix, 4% strand | P69924 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- DAT · 2'-deoxyadenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- FEO · Mu-oxo-diiron · ligand · 4 copies · chains E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
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 | 222 | 0.73 | 0.89 | 40 | DTP |
| 2 | 95 | 0.73 | 0.95 | 27 | empty |
| 3 | 444 | 0.73 | 0.83 | 67 | CDP |
| 4 | 235 | 0.73 | 0.88 | 41 | DTP |
| 5 | 223 | 0.72 | 0.88 | 45 | DTP |
Interfaces
8 interfaces between chains.
- E–H · 3231 Ų buried · 53 hydrogen bonds · protein-protein
- F–G · 3194 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 1733 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1724 Ų buried · 19 hydrogen bonds · protein-protein
- D–G · 1454 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5CNS · Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex… · the same entry in another collection · chain H against H, TM-score 1.00
- P00452 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 1 subunit… · a predicted model of the same protein · chain B 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 P00452
- Every structure of UniProt P69924
- Elsewhere: RCSB PDB 5CNS · PDBe 5CNS · UniProt P00452 · UniProt P69924
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