MolNFT v1 · #189422 · protein
Cryo-EM structure of pseudomonas aeruginosa rnap sigmas holoenzyme complexes
7VF9 · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of pseudomonas aeruginosa rnap sigmas holoenzyme complexes”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #189422 on GenesisL1…
- PDB
- 7VF9
- Type
- protein
- Length
- 3,425 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
- O52760, Q51561, Q9HWC9, Q9HTM1, P45684
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 21% helix, 37% strand | O52760 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 209 | 18% helix, 32% strand | O52760 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1324 | 30% helix, 20% strand | Q51561 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1339 | 33% helix, 14% strand | Q9HWC9 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 67 | 60% helix, 0% strand | Q9HTM1 |
| F | RNA polymerase sigma factor rpos | protein | 271 | 61% helix, 0% strand | P45684 |
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 | 863 | 0.83 | 0.85 | 84 | empty |
| 2 | 950 | 0.82 | 0.84 | 85 | empty |
| 3 | 1021 | 0.80 | 0.82 | 77 | empty |
| 4 | 759 | 0.79 | 0.82 | 91 | empty |
| 5 | 260 | 0.74 | 0.87 | 29 | empty |
Interfaces
9 interfaces between chains.
- C–D · 7902 Ų buried · 60 hydrogen bonds · protein-protein
- D–F · 2060 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1832 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1683 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 1334 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7VF9 · Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzyme complexes · the same entry in another collection · chain F against F, TM-score 1.00
- Q51561 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q51561) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q9HWC9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q9HWC9) · a predicted model of the same protein · chain D against A, TM-score 0.91
- O52760 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (O52760) · a predicted model of the same protein · chain A against A, TM-score 0.91
- P45684 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpos (P45684) · a predicted model of the same protein · chain F against A, TM-score 0.86
- Q9HTM1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q9HTM1) · a predicted model of the same protein · chain E against A, TM-score 0.85
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 O52760
- Every structure of UniProt Q51561
- Every structure of UniProt Q9HWC9
- Every structure of UniProt Q9HTM1
- Every structure of UniProt P45684
- Elsewhere: RCSB PDB 7VF9 · PDBe 7VF9 · UniProt O52760 · UniProt Q51561 · UniProt Q9HWC9 · UniProt Q9HTM1 · UniProt P45684
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