Research workbench
EM structure of bacillus subtilis ribonucleotide reductase inhibited filament composed of nrde alpha subunit and nrdf beta subunit with datp
Analyse EM structure of bacillus subtilis ribonucleotide reductase inhibited filament… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MW3
- Type
- protein
- Length
- 1,362 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase; Ribonucleoside-diphosphate reductase nrdf beta…
- EC
- 1.17.4.1
- UniProt
- A0A162Q3J9
- Ligands
- DTP
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 3 distinct chains · 42% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 673 | 42% helix, 9% strand | A0A162Q3J9 |
| D | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 673 | 42% helix, 9% strand | A0A162Q3J9 |
| I, J | Ribonucleoside-diphosphate reductase nrdf beta subunit | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.74 | 0.98 | 19 | empty |
| 2 | 209 | 0.73 | 0.89 | 37 | empty |
| 3 | 256 | 0.72 | 0.87 | 40 | empty |
| 4 | 56 | 0.72 | 0.98 | 19 | empty |
| 5 | 214 | 0.70 | 0.87 | 27 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1502 Ų buried · 6 hydrogen bonds · protein-protein
- D–J · 292 Ų buried · 4 hydrogen bonds · protein-protein
- C–I · 259 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MW3 · EM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of… · the same entry in another collection · chain C against C, 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 6MW3 · PDBe 6MW3 · UniProt A0A162Q3J9
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