Research workbench
The crystal structure of the BET3-TRS31-sedlin complex.
Analyse The crystal structure of the BET3-TRS31-sedlin complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J3W
- Type
- protein
- Length
- 926 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trafficking protein particle complex protein 2; Zgc 92866; Trafficking protein particle…
- UniProt
- Q9CQP2, Q6DGL5, O55013
- Ligands
- PLM
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trafficking protein particle complex protein 2 | protein | 142 | 44% helix, 24% strand | Q9CQP2 |
| B | Zgc 92866 | protein | 167 | 53% helix, 19% strand | Q6DGL5 |
| C | Trafficking protein particle complex protein 2 | protein | 135 | 39% helix, 26% strand | Q9CQP2 |
| D | Trafficking protein particle complex subunit 3 | protein | 157 | 50% helix, 19% strand | O55013 |
| E | Trafficking protein particle complex subunit 3 | protein | 158 | 50% helix, 20% strand | O55013 |
| F | Zgc 92866 | protein | 167 | 54% helix, 16% strand | Q6DGL5 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.80 | 0.93 | 30 | PLM |
| 2 | 237 | 0.77 | 0.90 | 32 | PLM |
| 3 | 779 | 0.76 | 0.80 | 91 | empty |
| 4 | 333 | 0.70 | 0.83 | 54 | empty |
| 5 | 265 | 0.56 | 0.77 | 32 | empty |
Interfaces
9 interfaces between chains.
- B–E · 1527 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1421 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 809 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 770 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 420 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid (palmitoylation).
Compared structures
- 2J3W · The crystal structure of the bet3-trs31-sedlin complex. · the same entry in another collection · chain F against F, TM-score 1.00
- O55013 · AlphaFold monomer V2.0 prediction for trafficking protein particle complex subunit 3… · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q9CQP2 · AlphaFold monomer V2.0 prediction for trafficking protein particle complex subunit 2… · a predicted model of the same protein · chain C 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 Q9CQP2
- Every structure of UniProt Q6DGL5
- Every structure of UniProt O55013
- Elsewhere: RCSB PDB 2J3W · PDBe 2J3W · UniProt Q9CQP2 · UniProt Q6DGL5 · UniProt O55013
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