MolNFT v1 · #136082 · protein + DNA
Crystal structure of aquifex aeolicus sigman bound to promoter DNA
5UI5 · DNA (31-mer): “Crystal structure of aquifex aeolicus sigman bound to promoter DNA”. X-ray diffraction, 17 pockets (best druggability 0.76). MolNFT v1 #136082 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UI5
- Type
- protein + DNA
- Length
- 761 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (31-mer); DNA (30-mer); RNA polymerase sigma factor rpon
- UniProt
- O66858
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | DNA (31-mer) | dna | 31 | — | — |
| B, O | DNA (30-mer) | dna | 30 | — | — |
| I | RNA polymerase sigma factor rpon | protein | 316 | 53% helix, 4% strand | O66858 |
| V | RNA polymerase sigma factor rpon | protein | 323 | 55% helix, 6% strand | O66858 |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.76 | 0.81 | 64 | empty |
| 2 | 109 | 0.75 | 0.95 | 27 | empty |
| 3 | 841 | 0.71 | 0.77 | 84 | empty |
| 4 | 499 | 0.59 | 0.74 | 48 | empty |
| 5 | 182 | 0.56 | 0.80 | 32 | empty |
Interfaces
7 interfaces between chains.
- I–V · 2036 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1354 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- N–O · 1332 Ų buried · 119 hydrogen bonds · nucleic-nucleic
- A–I · 907 Ų buried · 22 hydrogen bonds · protein-nucleic
- N–V · 787 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 5UI5 · Crystal structure of Aquifex aeolicus sigmaN bound to promoter DNA · the same entry in another collection · chain A against A, TM-score 1.00
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 O66858
- Elsewhere: RCSB PDB 5UI5 · PDBe 5UI5 · UniProt O66858
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