Research workbench
Crystal structure of the B30.2/SPRY domain of gustavus in complex with a 20-residue vasa peptide
Analyse Crystal structure of the B30.2/SPRY domain of gustavus in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IHS
- Type
- protein
- Length
- 433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG2944-pf, isoform F; 20-mer from ATP-dependent RNA helicase vasa
- EC
- 3.6.1.-
- UniProt
- Q7KRQ1, P09052
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG2944-pf, isoform F | protein | 203 | 8% helix, 43% strand | Q7KRQ1 |
| B | CG2944-pf, isoform F | protein | 195 | 9% helix, 45% strand | Q7KRQ1 |
| C | 20-mer from ATP-dependent RNA helicase vasa (EC 3.6.1.-) | protein | 15 | 0% helix, 7% strand | P09052 |
| D | 20-mer from ATP-dependent RNA helicase vasa (EC 3.6.1.-) | protein | 20 | 25% helix, 5% strand | P09052 |
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 | 441 | 0.69 | 0.80 | 47 | empty |
| 2 | 96 | 0.43 | 0.78 | 18 | empty |
| 3 | 52 | 0.28 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–D · 770 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 371 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2IHS · Crystal structure of the B30.2/SPRY domain of GUSTAVUS in complex with a 20-residue VASA… · the same entry in another collection · chain A against A, TM-score 1.00
- P09052 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase vasa (P09052) · a predicted model of the same protein · chain C against A, TM-score 0.31
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 Q7KRQ1
- Every structure of UniProt P09052
- Elsewhere: RCSB PDB 2IHS · PDBe 2IHS · UniProt Q7KRQ1 · UniProt P09052
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