Research workbench
AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpod (P00579)
Analyse AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpod (P00579) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- Accession
- P00579
- Type
- protein
- Length
- 613 residues
- Chains
- 1
- Collection
- MolNFT v1 / AlphaFold
- Contract
- 0xBf7491af3407816DFa88a5EA4c82e8A2B1D721eD
- Owner
- 0xd91633319BDB0a92cbC4f08DeA734Bf74C030064
- Molecule
- RNA polymerase sigma factor rpod
- UniProt
- P00579
- Pockets
- 5 · best druggability 0.72
Structure
1 distinct chain · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase sigma factor rpod | protein | 613 | 66% helix, 2% strand | P00579 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.72 | 0.76 | 60 | empty |
| 2 | 643 | 0.68 | 0.77 | 57 | empty |
| 3 | 377 | 0.62 | 0.78 | 44 | empty |
| 4 | 67 | 0.43 | 0.81 | 17 | empty |
| 5 | 102 | 0.36 | 0.73 | 15 | empty |
Compared structures
- 7BEF · Structures of class II bacterial transcription complexes · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 7W5Y · Cryo-EM structure of SoxS-dependent transcription activation complex with fpr promoter DNA · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 6B6H · The cryo-EM structure of a bacterial class I transcription activation complex · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 7W5X · Cryo-EM structure of SoxS-dependent transcription activation complex with zwf promoter DNA · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 4YLN · E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 4YLN · E. COLI transcription initiation complex - 17-bp spacer and 4-nt RNA · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 5W1T · X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 4JKR · Crystal structure of E. COLI RNA polymerase in complex with ppgpp · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 4JKR · Crystal Structure of E. coli RNA Polymerase in complex with ppGpp · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 4XSY · Crystal structure of CBR 9379 bound to Escherichia coli RNA polymerase holoenzyme · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 4XSY · Crystal structure of cbr 9379 bound to escherichia COLI RNA polymerase holoenzyme · an experimental structure of the same protein · chain A against F, TM-score 0.74
- 4YLP · E. COLI transcription initiation complex - 16-bp spacer and 5-nt RNA · an experimental structure of the same protein · chain A against F, TM-score 0.73
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 P00579
- Elsewhere: UniProt P00579 · AlphaFold DB P00579
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