Research workbench
Ribonucleotide reductase Y730NO2Y modified R1 subunit of E. COLI
Analyse Ribonucleotide reductase Y730NO2Y modified R1 subunit of E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XAK
- Type
- protein
- Length
- 2,235 residues
- Chains
- 7
- 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
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 728 | 46% helix, 12% strand | P00452 |
| D, E, F | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 16 | 25% helix, 13% strand | P69924 |
| P | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 3 | 0% helix, 0% strand | P69924 |
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.75 | 0.92 | 28 | empty |
| 2 | 891 | 0.73 | 0.77 | 85 | empty |
| 3 | 796 | 0.72 | 0.78 | 89 | empty |
| 4 | 666 | 0.68 | 0.76 | 57 | empty |
| 5 | 161 | 0.59 | 0.83 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1178 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 873 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 873 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 870 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 2XAK · Ribonucleotide reductase Y730NO2Y modified R1 subunit of E. coli · the same entry in another collection · chain F against F, 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 0.99
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 2XAK · PDBe 2XAK · UniProt P00452 · UniProt P69924
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