Research workbench
Cryo-EM structure of pseudomonas aeruginosa rnap sigmas holoenzyme complexes with transcription factor suta (closed lobe)
Analyse Cryo-EM structure of pseudomonas aeruginosa rnap sigmas holoenzyme complexes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XL4
- Type
- protein
- Length
- 3,479 residues
- Chains
- 7
- 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, Q9HTR9, P45684
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 20% helix, 34% strand | O52760 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 212 | 19% helix, 33% strand | O52760 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1324 | 27% helix, 21% strand | Q51561 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1339 | 32% helix, 15% strand | Q9HWC9 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 70 | 54% helix, 0% strand | Q9HTM1 |
| G | Transcriptional factor suta | protein | 31 | 61% helix, 6% strand | Q9HTR9 |
| F | RNA polymerase sigma factor rpos | protein | 278 | 63% 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 | 1006 | 0.84 | 0.85 | 104 | empty |
| 2 | 1076 | 0.80 | 0.82 | 115 | empty |
| 3 | 1087 | 0.80 | 0.81 | 110 | empty |
| 4 | 1080 | 0.79 | 0.80 | 126 | empty |
| 5 | 1193 | 0.78 | 0.80 | 83 | empty |
Interfaces
10 interfaces between chains.
- C–D · 8016 Ų buried · 67 hydrogen bonds · protein-protein
- D–F · 2173 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1819 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1792 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 1298 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7XL4 · Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzyme complexes with… · 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 0.95
- 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 0.92
- 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 0.90
- 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 0.87
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 Q9HTR9
- Every structure of UniProt P45684
- Elsewhere: RCSB PDB 7XL4 · PDBe 7XL4 · UniProt O52760 · UniProt Q51561 · UniProt Q9HWC9 · UniProt Q9HTM1 · UniProt Q9HTR9 · UniProt P45684
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