Research workbench
Cryo-EM structure of E. COLI rnap SIGMA70 holoenzyme
Analyse Cryo-EM structure of E. COLI rnap SIGMA70 holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C9Y
- Type
- protein
- Length
- 3,685 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 17% helix, 33% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 19% helix, 35% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1350 | 37% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 62% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 468 | 63% helix, 1% strand | P00579 |
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 | 837 | 0.83 | 0.85 | 83 | empty |
| 2 | 798 | 0.82 | 0.85 | 73 | empty |
| 3 | 388 | 0.77 | 0.87 | 48 | empty |
| 4 | 561 | 0.77 | 0.84 | 47 | empty |
| 5 | 1130 | 0.76 | 0.78 | 86 | empty |
Interfaces
9 interfaces between chains.
- C–D · 8141 Ų buried · 75 hydrogen bonds · protein-protein
- D–F · 2682 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2001 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1863 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1780 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6C9Y · Cryo-EM structure of E. coli RNAP sigma70 holoenzyme · the same entry in another collection · chain C against C, 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 C against A, TM-score 0.98
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
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 6C9Y · PDBe 6C9Y · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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