Research workbench
Crystal structure of virb core domain complexed with the cis-acting site upstream icsp 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
- 3W2A
- Type
- protein + DNA
- Length
- 160 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virulence regulon transcriptional activator virb; DNA (31-mer)
- UniProt
- P0A247
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virulence regulon transcriptional activator virb | protein | 114 | 61% helix, 0% strand | P0A247 |
| B | DNA (31-mer) | dna | 23 | — | — |
| C | DNA (31-mer) | dna | 23 | — | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.45 | 0.77 | 15 | empty |
| 2 | 182 | 0.44 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 986 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- A–B · 395 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 289 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (engineered).
Compared structures
- 3W2A · Crystal structure of VirB core domain complexed with the cis-acting site upstream icsp… · 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 0.95
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 3W2A · PDBe 3W2A · UniProt P0A247
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