Research workbench
Crystal structure of virb core domain complexed with the cis-acting site upstream icsb promoter
Analyse Crystal structure of virb core domain complexed with the cis-acting site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W3C
- Type
- protein + DNA
- Length
- 168 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virulence regulon transcriptional activator virb; DNA (26-mer)
- UniProt
- P0A247
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virulence regulon transcriptional activator virb | protein | 116 | 66% helix, 0% strand | P0A247 |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.51 | 0.80 | 17 | empty |
| 2 | 142 | 0.39 | 0.74 | 14 | empty |
| 3 | 115 | 0.36 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1030 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- A–B · 419 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 323 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 3W3C · Crystal structure of VirB core domain complexed with the cis-acting site upstream icsb… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A247 · AlphaFold monomer V2.0 prediction for virulence regulon transcriptional activator virb… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P0A247
- Elsewhere: RCSB PDB 3W3C · PDBe 3W3C · UniProt P0A247
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