MolNFT v1 · #157433 · protein
EM structure of bacillus subtilis ribonucleotide reductase inhibited double-helical filament of nrde alpha subunit with datp
6MYX · Ribonucleoside-diphosphate reductase: “EM structure of bacillus subtilis ribonucleotide reductase inhibited double-helical filament of nrde alpha…”. Electron microscopy, 1 ligand (DTP), 20 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 6MYX
- Type
- protein
- Length
- 2,692 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase
- EC
- 1.17.4.1
- UniProt
- A0A162Q3J9
- Ligands
- DTP
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, I, J | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 673 | 44% helix, 9% strand | A0A162Q3J9 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 8 copies · chains C, D, I, J
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 | 88 | 0.76 | 0.97 | 27 | empty |
| 2 | 82 | 0.75 | 0.97 | 22 | empty |
| 3 | 78 | 0.75 | 0.97 | 24 | empty |
| 4 | 73 | 0.74 | 0.97 | 20 | empty |
| 5 | 78 | 0.73 | 0.96 | 23 | empty |
Interfaces
3 interfaces between chains.
- I–J · 1566 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1519 Ų buried · 14 hydrogen bonds · protein-protein
- C–J · 134 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6MYX · EM structure of Bacillus subtilis ribonucleotide reductase inhibited double-helical… · the same entry in another collection · chain J against J, TM-score 1.00
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 A0A162Q3J9
- Elsewhere: RCSB PDB 6MYX · PDBe 6MYX · UniProt A0A162Q3J9
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