Research workbench
Structures of class I bacterial transcription complexes
Analyse Structures of class I bacterial transcription complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BEG
- Type
- protein + DNA
- Length
- 4,189 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
- P0A7Z4, P0A8V4, P0A8T8, P0A800, Q0P6L9, Q48413
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 9 distinct chains · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 305 | 24% helix, 26% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 302 | 25% helix, 21% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 28% helix, 17% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1362 | 35% helix, 12% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 70% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 496 | 65% helix, 0% strand | Q0P6L9 |
| N | Class I pacra promoter non-template DNA | dna | 94 | — | — |
| T | Class I pacra promoter template DNA | dna | 94 | — | — |
| G | Transcriptional activator rama | protein | 105 | 58% helix, 0% strand | Q48413 |
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 | 1050 | 0.86 | 0.87 | 117 | empty |
| 2 | 952 | 0.85 | 0.86 | 86 | empty |
| 3 | 735 | 0.84 | 0.88 | 82 | empty |
| 4 | 847 | 0.83 | 0.85 | 101 | empty |
| 5 | 705 | 0.83 | 0.87 | 77 | empty |
Interfaces
23 interfaces between chains.
- C–D · 8119 Ų buried · 57 hydrogen bonds · protein-protein
- N–T · 3761 Ų buried · 305 hydrogen bonds · nucleic-nucleic
- D–F · 2992 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 2385 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2017 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7BEG · Structures of class I bacterial transcription complexes · the same entry in another collection · chain G against G, TM-score 1.00
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain D against A, TM-score 0.92
- Q48413 · AlphaFold monomer V2.0 prediction for transcriptional activator rama (Q48413) · a predicted model of the same protein · chain G against A, TM-score 0.77
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 P0A8V4
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0A800
- Every structure of UniProt Q0P6L9
- Every structure of UniProt Q48413
- Elsewhere: RCSB PDB 7BEG · PDBe 7BEG · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T8 · UniProt P0A800 · UniProt Q0P6L9 · UniProt Q48413
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