Research workbench
Crystal structure of DMNXF2 uba domain fused with panoramix helix
Analyse Crystal structure of DMNXF2 uba domain fused with panoramix helix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OPF
- Type
- protein
- Length
- 342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear RNA export factor 2, panoramix fusion
- UniProt
- Q9VV73, Q9W2H9
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear RNA export factor 2, panoramix fusion | protein | 85 | 78% helix, 2% strand | Q9VV73, Q9W2H9 |
| B | Nuclear RNA export factor 2, panoramix fusion | protein | 84 | 79% helix, 2% strand | Q9VV73, Q9W2H9 |
| D | Nuclear RNA export factor 2, panoramix fusion | protein | 86 | 72% helix, 0% strand | Q9VV73, Q9W2H9 |
| F | Nuclear RNA export factor 2, panoramix fusion | protein | 87 | 70% helix, 0% strand | Q9VV73, Q9W2H9 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.68 | 0.77 | 65 | empty |
| 2 | 461 | 0.61 | 0.75 | 39 | empty |
| 3 | 55 | 0.40 | 0.81 | 13 | empty |
| 4 | 57 | 0.27 | 0.74 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 665 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 514 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 499 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 126 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 120 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6OPF · Crystal structure of dmNxf2 UBA domain fused with Panoramix helix · the same entry in another collection · chain A against A, TM-score 1.00
- Q9VV73 · AlphaFold monomer V2.0 prediction for nuclear RNA export factor 2 (Q9VV73) · a predicted model of the same protein · chain B against A, TM-score 0.66
- Q9W2H9 · AlphaFold monomer V2.0 prediction for protein panoramix (Q9W2H9) · a predicted model of the same protein · chain B against A, TM-score 0.32
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 Q9VV73
- Every structure of UniProt Q9W2H9
- Elsewhere: RCSB PDB 6OPF · PDBe 6OPF · UniProt Q9VV73 · UniProt Q9W2H9
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