Research workbench
Pandda analysis group deposition -- AAR2/RNASEH in complex with fragment F2X-entry D07A
Analyse Pandda analysis group deposition -- AAR2/RNASEH in complex with fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QYC
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor 8; A1 cistron-splicing factor AAR2
- UniProt
- P33334, P32357
- Ligands
- SYJ, SO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor 8 | protein | 254 | 47% helix, 18% strand | P33334 |
| B | A1 cistron-splicing factor AAR2 | protein | 300 | 45% helix, 20% strand | P32357 |
Ligands and binding sites
- SYJ · 2-fluoranyl-~{N}-(furan-2-ylmethyl)benzenesulfonamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PGR · R-1,2-propanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.59 | 0.78 | 24 | empty |
| 2 | 83 | 0.40 | 0.78 | 18 | empty |
| 3 | 104 | 0.39 | 0.76 | 16 | empty |
| 4 | 68 | 0.37 | 0.78 | 15 | empty |
| 5 | 106 | 0.36 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5QYC · PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry D07a · the same entry in another collection · chain A against A, TM-score 1.00
- P32357 · AlphaFold monomer V2.0 prediction for A1 cistron-splicing factor AAR2 (P32357) · a predicted model of the same protein · chain B 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 P33334
- Every structure of UniProt P32357
- Elsewhere: RCSB PDB 5QYC · PDBe 5QYC · UniProt P33334 · UniProt P32357
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