Research workbench
PanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 33, DMSO-free
Analyse PanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5R1I
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.01
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- Pre-mRNA-splicing factor 8; A1 cistron-splicing factor AAR2
- UniProt
- P33334, P32357
- Pockets
- 6 · best druggability 0.43
Structure
x-ray diffraction · resolution 2.01 · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor 8 | protein | 237 | 45% helix, 20% strand | P33334 |
| B | A1 cistron-splicing factor AAR2 | protein | 300 | 44% helix, 19% strand | P32357 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.43 | 0.80 | 18 | empty |
| 2 | 113 | 0.38 | 0.75 | 16 | empty |
| 3 | 75 | 0.38 | 0.77 | 16 | empty |
| 4 | 115 | 0.37 | 0.74 | 19 | empty |
| 5 | 85 | 0.36 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 487 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5R1I · Pandda analysis group deposition -- auto-refined data of AAR2/RNASEH for ground state… · 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
- P33334 · AlphaFold monomer V2.0 prediction for pre-mRNA-splicing factor 8 (P33334) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 5R1I · PDBe 5R1I · UniProt P33334 · UniProt P32357
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