Research workbench
Crystal structure and mutational analysis of the NXF2/NXT1 heterodimeric complex from caenorhabditis elegans at 1.84 a resolution
Analyse Crystal structure and mutational analysis of the NXF2/NXT1 heterodimeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NV0
- Type
- protein
- Length
- 332 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear RNA export factor 2; NTF2-related export protein
- UniProt
- Q9XVS8, Q9U757
- Ligands
- NA
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear RNA export factor 2 | protein | 196 | 35% helix, 28% strand | Q9XVS8 |
| B | NTF2-related export protein | protein | 136 | 35% helix, 43% strand | Q9U757 |
Ligands and binding sites
- NA · Sodium ion · metal · 19 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- BME · Beta-mercaptoethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.59 | 0.89 | 19 | BME |
| 2 | 228 | 0.54 | 0.77 | 37 | PEG, NA |
| 3 | 68 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1883 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3NV0 · Crystal structure and mutational analysis of the NXF2/NXT1 heterodimeric complex from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U757 · AlphaFold monomer V2.0 prediction for NTF2-related export protein (Q9U757) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q9XVS8 · AlphaFold monomer V2.0 prediction for nuclear RNA export factor 2 (Q9XVS8) · 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 Q9XVS8
- Every structure of UniProt Q9U757
- Elsewhere: RCSB PDB 3NV0 · PDBe 3NV0 · UniProt Q9XVS8 · UniProt Q9U757
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