MolNFT v1 · #115575 · protein
Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex bound to ADP and dgtp at 3.40 ångströms resolution
5CNU · Ribonucleoside-diphosphate reductase 1 subunit alpha: “Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex bound to ADP and…”. X-ray diffraction, 5 ligands (DGT, ADP, DAT), 20 pockets (best…
- PDB
- 5CNU
- Type
- protein
- Length
- 4,352 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase 1 subunit alpha; Ribonucleoside-diphosphate…
- EC
- 1.17.4.1
- UniProt
- P00452, P69924
- Ligands
- DGT, ADP, DAT, FEO, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 732 | 45% helix, 13% strand | P00452 |
| B, C, D | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 733 | 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 | 67% helix, 4% strand | P69924 |
| H | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 355 | 67% helix, 4% strand | P69924 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- DAT · 2'-deoxyadenosine-5'-diphosphate · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.80 | 0.85 | 107 | DGT, ADP |
| 2 | 662 | 0.79 | 0.84 | 104 | ADP, DGT |
| 3 | 560 | 0.78 | 0.85 | 81 | DGT, ADP |
| 4 | 101 | 0.73 | 0.94 | 26 | empty |
| 5 | 231 | 0.72 | 0.88 | 45 | DGT |
Interfaces
8 interfaces between chains.
- F–G · 3229 Ų buried · 50 hydrogen bonds · protein-protein
- E–H · 3207 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 1731 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1670 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 1426 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 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 0.98
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 P00452
- Every structure of UniProt P69924
- Elsewhere: RCSB PDB 5CNU · PDBe 5CNU · UniProt P00452 · UniProt P69924
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