MolNFT v1 · #125263 · protein
Structure of the saccharomyces cerevisiae trex-2 complex
5L3T · Nuclear mRNA export protein SAC3: “Structure of the saccharomyces cerevisiae trex-2 complex”. X-ray diffraction, 18 pockets (best druggability 0.60). MolNFT v1 #125263 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L3T
- Type
- protein
- Length
- 849 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
- Pockets
- 18 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear mRNA export protein SAC3 | protein | 294 | 63% helix, 2% strand | P46674 |
| B | Nuclear mRNA export protein THP1 | protein | 455 | 64% helix, 3% strand | Q08231 |
| C | 26S proteasome complex subunit SEM1 | protein | 48 | 42% helix, 2% strand | O94742 |
| D | SAC3POLYALA | protein | 17 | 88% helix, 0% strand | — |
| E | SAC3POLYALA | protein | 24 | 88% helix, 0% strand | — |
| F | SAC3POLYALA | protein | 11 | 82% helix, 0% strand | — |
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.60 | 0.88 | 22 | empty |
| 2 | 343 | 0.59 | 0.77 | 32 | empty |
| 3 | 161 | 0.53 | 0.79 | 27 | empty |
| 4 | 164 | 0.51 | 0.79 | 24 | empty |
| 5 | 224 | 0.51 | 0.76 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2391 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2384 Ų buried · 40 hydrogen bonds · protein-protein
- A–F · 165 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 94 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5L3T · Structure of the Saccharomyces cerevisiae TREX-2 complex · 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 0.99
- 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 0.53
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 5L3T · PDBe 5L3T · UniProt P46674 · UniProt Q08231 · UniProt O94742
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