MolNFT v1 · #144968 · protein + DNA
Cryo-EM structure of E. COLI rnap SIGMA70 open complex
6CA0 · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of E. COLI rnap SIGMA70 open complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #144968 on GenesisL1: 3D structure, binding…
- PDB
- 6CA0
- Type
- protein + DNA
- Length
- 3,800 residues
- Chains
- 10
- 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 0.85
Structure
electron microscopy · 10 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 22% helix, 39% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 41% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 32% helix, 22% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1352 | 37% helix, 15% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 61% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 472 | 69% helix, 1% strand | P00579 |
| G | DNA (45-mer) | dna | 45 | — | — |
| H | DNA (35-mer) | dna | 35 | — | — |
| I | DNA (5'-D(P*TP*CP*TP*GP*AP*CP*GP*CP*GP*GP*C)-3') | dna | 11 | — | — |
| J | DNA (5'-D(P*GP*CP*CP*GP*CP*GP*TP*CP*AP*GP*A)-3') | dna | 11 | — | — |
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 | 1163 | 0.85 | 0.86 | 130 | empty |
| 2 | 1157 | 0.84 | 0.85 | 126 | empty |
| 3 | 396 | 0.80 | 0.89 | 56 | empty |
| 4 | 538 | 0.79 | 0.86 | 63 | empty |
| 5 | 862 | 0.79 | 0.82 | 82 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8228 Ų buried · 95 hydrogen bonds · protein-protein
- D–F · 2636 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2032 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1856 Ų buried · 37 hydrogen bonds · protein-nucleic
- C–F · 1837 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6CA0 · Cryo-EM structure of E. coli RNAP sigma70 open complex · the same entry in another collection · chain J against J, 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 6CA0 · PDBe 6CA0 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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