Research workbench
Structure of the NUP82-NUP159-NUP98 heterotrimer
Analyse Structure of the NUP82-NUP159-NUP98 heterotrimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TKN
- Type
- protein
- Length
- 1,870 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin NUP82; Nucleoporin NUP159; Nucleoporin 98
- UniProt
- P40368, P40477, Q6PFD9
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoporin NUP82 | protein | 451 | 13% helix, 34% strand | P40368 |
| B, E, H | Nucleoporin NUP159 | protein | 28 | 82% helix, 0% strand | P40477 |
| C, F, I | Nucleoporin 98 | protein | 147 | 16% helix, 33% strand | Q6PFD9 |
| D, G | Nucleoporin NUP82 | protein | 447 | 14% helix, 34% strand | P40368 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.83 | 0.84 | 125 | empty |
| 2 | 1049 | 0.79 | 0.80 | 79 | empty |
| 3 | 1167 | 0.77 | 0.79 | 82 | empty |
| 4 | 1185 | 0.77 | 0.79 | 78 | empty |
| 5 | 419 | 0.68 | 0.80 | 48 | empty |
Interfaces
19 interfaces between chains.
- D–F · 1257 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1198 Ų buried · 20 hydrogen bonds · protein-protein
- G–I · 1186 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 977 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 950 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3TKN · Structure of the Nup82-Nup159-Nup98 heterotrimer · the same entry in another collection · chain I against I, TM-score 1.00
- P40368 · AlphaFold monomer V2.0 prediction for nucleoporin NUP82 (P40368) · a predicted model of the same protein · chain D against A, TM-score 1.00
- Q6PFD9 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP98-NUP96 (Q6PFD9) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P40368
- Every structure of UniProt P40477
- Every structure of UniProt Q6PFD9
- Elsewhere: RCSB PDB 3TKN · PDBe 3TKN · UniProt P40368 · UniProt P40477 · UniProt Q6PFD9
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