Research workbench
Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10 promoter element ssdna
Analyse Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KI2
- Type
- protein + DNA
- Length
- 439 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'); RNA polymerase sigma factor
- UniProt
- Q9EZJ8
- Ligands
- K
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3') | dna | 11 | — | — |
| E | DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3') | dna | 10 | — | — |
| F, G | DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3') | dna | 3 | — | — |
| A | RNA polymerase sigma factor | protein | 178 | 73% helix, 0% strand | Q9EZJ8 |
| B | RNA polymerase sigma factor | protein | 234 | 69% helix, 0% strand | Q9EZJ8 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 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 | 0.74 | 0.78 | 96 | empty |
| 2 | 230 | 0.52 | 0.76 | 37 | empty |
| 3 | 107 | 0.51 | 0.82 | 19 | empty |
| 4 | 108 | 0.37 | 0.74 | 27 | empty |
| 5 | 67 | 0.33 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- E–B · 940 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–A · 919 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 586 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 109 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- D–G · 106 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 4KI2 · Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10… · 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 0.88
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 4KI2 · PDBe 4KI2 · UniProt Q9EZJ8
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