Research workbench
Crystal structure of virb core domain (se-met derivative) complexed with the cis-acting site (5-bru modifications) upstream icsb promoter
Analyse Crystal structure of virb core domain (se-met derivative) complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VWB
- 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 0.52
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virulence regulon transcriptional activator virb | protein | 116 | 65% helix, 0% strand | P0A247 |
| C | DNA (26-mer) | dna | 26 | — | — |
| B | 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 | 154 | 0.52 | 0.79 | 22 | empty |
| 2 | 113 | 0.34 | 0.73 | 17 | empty |
| 3 | 52 | 0.25 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1012 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–B · 426 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 343 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3VWB · Crystal structure of VirB core domain (Se-Met derivative) complexed with the cis-acting… · 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 3VWB · PDBe 3VWB · UniProt P0A247
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