MolNFT v1 · #115574 · protein
Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex bound to udp and datp at 3.25 ångströms resolution
5CNT · Ribonucleoside-diphosphate reductase 1 subunit alpha: “Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex bound to udp and…”. X-ray diffraction, 4 ligands (DTP, UDP, FEO), 20 pockets (best…
- PDB
- 5CNT
- Type
- protein
- Length
- 4,354 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
- DTP, UDP, FEO, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 734 | 46% helix, 14% strand | P00452 |
| D | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 733 | 45% helix, 14% strand | P00452 |
| E | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 350 | 68% helix, 4% strand | P69924 |
| F, G | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 357 | 66% 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
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 12 copies · chains A, B, C, D
- UDP · Uridine-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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.74 | 0.84 | 74 | UDP |
| 2 | 123 | 0.72 | 0.92 | 29 | empty |
| 3 | 442 | 0.71 | 0.82 | 64 | UDP |
| 4 | 123 | 0.71 | 0.92 | 26 | empty |
| 5 | 63 | 0.70 | 0.97 | 21 | empty |
Interfaces
8 interfaces between chains.
- E–H · 3195 Ų buried · 51 hydrogen bonds · protein-protein
- F–G · 3192 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 1699 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1694 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 1465 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5CNT · 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 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 P00452
- Every structure of UniProt P69924
- Elsewhere: RCSB PDB 5CNT · PDBe 5CNT · UniProt P00452 · UniProt P69924
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