Research workbench
Electron cryo-microscopy of an RNA polymerase
Analyse Electron cryo-microscopy of an RNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J9B
- Type
- protein + RNA
- Length
- 1,974 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase; RNA-directed RNA polymerase catalytic subunit; Polymerase basic protein 2…
- EC
- 2.7.7.48
- UniProt
- Q91R78, Q9Q0V0
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Polymerase | protein | 471 | 47% helix, 16% strand | Q91R78 |
| B, I | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 440 | 62% helix, 6% strand | Q9Q0V0 |
| C, J | Polymerase basic protein 2 | protein | 66 | 82% helix, 0% strand | — |
| D, K | RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') | rna | 5 | — | — |
| E | RNA (5'-R(*UP*UP*UP*UP*UP*A)-3') | rna | 5 | — | — |
| L | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | rna | 5 | — | — |
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 | 193 | 0.81 | 0.95 | 39 | empty |
| 2 | 800 | 0.79 | 0.83 | 119 | empty |
| 3 | 155 | 0.79 | 0.95 | 30 | empty |
| 4 | 185 | 0.72 | 0.89 | 32 | empty |
| 5 | 410 | 0.72 | 0.83 | 75 | empty |
Interfaces
13 interfaces between chains.
- H–I · 3373 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3372 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 172 Ų buried · 1 hydrogen bond · protein-protein
- K–L · 161 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–J · 126 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3J9B · Electron cryo-microscopy of an RNA polymerase · the same entry in another collection · chain A against A, 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 Q91R78
- Every structure of UniProt Q9Q0V0
- Elsewhere: RCSB PDB 3J9B · PDBe 3J9B · UniProt Q91R78 · UniProt Q9Q0V0
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