Research workbench
Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssdna oligo (tataat)
Analyse Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UGP
- Type
- protein + DNA
- Length
- 194 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase sigma factor; 5'-D(*TP*GP*TP*AP*TP*AP*AP*TP*GP*GP*G)-3'
- UniProt
- Q9EZJ8
- Ligands
- K
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase sigma factor | protein | 179 | 74% helix, 0% strand | Q9EZJ8 |
| B | 5'-D(*TP*GP*TP*AP*TP*AP*AP*TP*GP*GP*G)-3' | dna | 10 | — | — |
| C | 5'-D(*TP*GP*TP*AP*TP*AP*AP*TP*GP*GP*G)-3' | dna | 5 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.61 | 0.88 | 18 | empty |
| 2 | 67 | 0.35 | 0.77 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 950 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 108 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 3UGP · Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9EZJ8 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (Q9EZJ8) · a predicted model of the same protein · chain A 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 Q9EZJ8
- Elsewhere: RCSB PDB 3UGP · PDBe 3UGP · UniProt Q9EZJ8
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