Research workbench
Crystal structure of the datp inhibited E. COLI class ia ribonucleotide reductase complex at 4 ångströms resolution
Analyse Crystal structure of the datp inhibited E. COLI class ia ribonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ERM
- Type
- protein
- Length
- 4,351 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, DAT, FEO, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 733 | 45% helix, 12% strand | P00452 |
| B | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 734 | 46% helix, 10% strand | P00452 |
| C | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 731 | 45% helix, 11% strand | P00452 |
| D | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 733 | 45% helix, 12% strand | P00452 |
| E | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 352 | 66% helix, 3% strand | P69924 |
| F, G | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 356 | 66% helix, 4% strand | P69924 |
| H | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 356 | 67% helix, 3% strand | P69924 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 8 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 · 4 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 | 996 | 0.79 | 0.80 | 99 | DAT, DTP |
| 2 | 1058 | 0.78 | 0.80 | 103 | DTP, DAT |
| 3 | 1034 | 0.77 | 0.79 | 99 | DAT, DTP |
| 4 | 812 | 0.75 | 0.80 | 77 | DTP, DAT |
| 5 | 175 | 0.74 | 0.91 | 27 | empty |
Interfaces
8 interfaces between chains.
- F–G · 3094 Ų buried · 44 hydrogen bonds · protein-protein
- E–H · 3069 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 1498 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 1444 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 1426 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4ERM · 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 4ERM · PDBe 4ERM · UniProt P00452 · UniProt P69924
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