Research workbench
Cryo-EM structure of pseudomonas aeruginosa suta transcription activation complex
Analyse Cryo-EM structure of pseudomonas aeruginosa suta transcription activation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F0R
- Type
- protein + DNA
- Length
- 3,544 residues
- Chains
- 9
- 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 0.87
Structure
electron microscopy · 9 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 19% helix, 29% strand | O52760 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 209 | 20% helix, 29% strand | O52760 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1324 | 28% helix, 19% strand | Q51561 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1339 | 33% helix, 13% strand | Q9HWC9 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 67 | 54% helix, 0% strand | Q9HTM1 |
| G | Transcriptional factor suta | protein | 34 | 56% helix, 0% strand | Q9HTR9 |
| F | RNA polymerase sigma factor rpos | protein | 278 | 57% helix, 0% strand | P45684 |
| I | DNA (70-mer) | dna | 38 | — | — |
| H | DNA (70-mer) | dna | 40 | — | — |
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 | 1175 | 0.87 | 0.87 | 151 | empty |
| 2 | 1019 | 0.86 | 0.87 | 126 | empty |
| 3 | 684 | 0.84 | 0.88 | 80 | empty |
| 4 | 654 | 0.83 | 0.88 | 83 | empty |
| 5 | 510 | 0.83 | 0.90 | 58 | empty |
Interfaces
18 interfaces between chains.
- C–D · 8498 Ų buried · 75 hydrogen bonds · protein-protein
- D–F · 2636 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 2308 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 1929 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1891 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7F0R · Cryo-EM structure of Pseudomonas aeruginosa SutA transcription activation complex · 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 0.92
- O52760 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (O52760) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 7F0R · PDBe 7F0R · UniProt O52760 · UniProt Q51561 · UniProt Q9HWC9 · UniProt Q9HTM1 · UniProt Q9HTR9 · UniProt P45684
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