Research workbench
Crystal structure of SAC3/THP1/SEM1
Analyse Crystal structure of SAC3/THP1/SEM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TRQ
- Type
- protein
- Length
- 1,268 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear mRNA export protein SAC3; Nuclear mRNA export protein THP1; 26S proteasome…
- UniProt
- P46674, Q08231, O94742
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nuclear mRNA export protein SAC3 | protein | 299 | 61% helix, 2% strand | P46674 |
| B, E | Nuclear mRNA export protein THP1 | protein | 286 | 64% helix, 4% strand | Q08231 |
| C, F | 26S proteasome complex subunit SEM1 | protein | 49 | 33% helix, 2% strand | O94742 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.70 | 0.80 | 63 | empty |
| 2 | 509 | 0.70 | 0.80 | 54 | empty |
| 3 | 323 | 0.59 | 0.77 | 35 | empty |
| 4 | 139 | 0.59 | 0.84 | 21 | empty |
| 5 | 370 | 0.58 | 0.75 | 29 | empty |
Interfaces
8 interfaces between chains.
- D–E · 2422 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2407 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2372 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2228 Ų buried · 31 hydrogen bonds · protein-protein
- B–E · 925 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4TRQ · Crystal structure of Sac3/Thp1/Sem1 · the same entry in another collection · chain F against F, TM-score 1.00
- P46674 · AlphaFold monomer V2.0 prediction for nuclear mRNA export protein SAC3 (P46674) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q08231 · AlphaFold monomer V2.0 prediction for nuclear mRNA export protein THP1 (Q08231) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O94742 · AlphaFold monomer V2.0 prediction for 26S proteasome complex subunit SEM1 (O94742) · a predicted model of the same protein · chain C against A, TM-score 0.48
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 P46674
- Every structure of UniProt Q08231
- Every structure of UniProt O94742
- Elsewhere: RCSB PDB 4TRQ · PDBe 4TRQ · UniProt P46674 · UniProt Q08231 · UniProt O94742
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