Research workbench
Crystal structure of the TNPO3 - CPSF6 rsld complex
Analyse Crystal structure of the TNPO3 - CPSF6 rsld complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GX9
- Type
- protein
- Length
- 1,841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transportin-3; Cleavage and polyadenylation specificity factor subunit 6
- UniProt
- Q9Y5L0, Q16630
- Ligands
- BCN, BEN, MG
- Pockets
- 20 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transportin-3 | protein | 912 | 75% helix, 0% strand | Q9Y5L0 |
| B | Transportin-3 | protein | 911 | 75% helix, 0% strand | Q9Y5L0 |
| C, D | Cleavage and polyadenylation specificity factor subunit 6 | protein | 9 | 0% helix, 0% strand | Q16630 |
Ligands and binding sites
- BCN · Bicine · ligand · 2 copies · chains A, B
- BEN · Benzamidine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.57 | 0.79 | 28 | empty |
| 2 | 66 | 0.56 | 0.88 | 16 | BCN |
| 3 | 66 | 0.56 | 0.88 | 16 | BCN |
| 4 | 103 | 0.55 | 0.85 | 18 | empty |
| 5 | 87 | 0.54 | 0.86 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 709 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 708 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 331 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 6GX9 · Crystal structure of the TNPO3 - CPSF6 RSLD complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y5L0 · AlphaFold monomer V2.0 prediction for transportin-3 (Q9Y5L0) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q16630 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain D against A, TM-score 0.43
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 Q9Y5L0
- Every structure of UniProt Q16630
- Elsewhere: RCSB PDB 6GX9 · PDBe 6GX9 · UniProt Q9Y5L0 · UniProt Q16630
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