Research workbench
CryoEM structure of E.coli his pause elongation complex without pause hairpin
Analyse CryoEM structure of E.coli his pause elongation complex without pause hairpin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BJS
- Type
- protein + DNA + RNA
- Length
- 3,239 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 5.5
- Source
- Escherichia coli (strain K12); SYNTHETIC CONSTRUCT
- Molecule
- DNA (32-mer); RNA (29-mer); DNA-directed RNA polymerase subunit alpha; DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 5.5 · 8 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (32-mer) | dna | 23 | — | — |
| B | DNA (32-mer) | dna | 31 | — | — |
| R | RNA (29-mer) | rna | 11 | — | — |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 20% helix, 35% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 20% helix, 38% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1316 | 30% helix, 19% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1337 | 37% helix, 16% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | P0A800 |
Ligands and binding sites
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 | 572 | 0.85 | 0.91 | 76 | empty |
| 2 | 858 | 0.84 | 0.86 | 101 | empty |
| 3 | 620 | 0.83 | 0.89 | 69 | empty |
| 4 | 534 | 0.80 | 0.87 | 45 | empty |
| 5 | 230 | 0.80 | 0.92 | 49 | empty |
Interfaces
16 interfaces between chains.
- I–J · 7659 Ų buried · 84 hydrogen bonds · protein-protein
- G–H · 1857 Ų buried · 19 hydrogen bonds · protein-protein
- G–I · 1759 Ų buried · 21 hydrogen bonds · protein-protein
- J–K · 1246 Ų buried · 15 hydrogen bonds · protein-protein
- B–J · 969 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6BJS · Cryoem structure of E.COLI his pause elongation complex without pause hairpin · the same entry in another collection · chain R against R, TM-score 1.00
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain I against A, TM-score 0.99
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain J against A, TM-score 0.94
- P0A800 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A800) · a predicted model of the same protein · chain K against A, TM-score 0.91
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 6BJS · PDBe 6BJS · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800
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