MolNFT v1 · #119753 · protein
Structure of the saccharomyces cerevisiae trex-2 complex
5G5P · Nuclear mRNA export protein SAC3: “Structure of the saccharomyces cerevisiae trex-2 complex”. Electron microscopy, 15 pockets (best druggability 0.62). MolNFT v1 #119753 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G5P
- Type
- protein
- Length
- 849 residues
- Chains
- 6
- Method
- electron microscopy
- 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
- 15 · best druggability 0.62
Structure
electron microscopy · 6 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear mRNA export protein SAC3 | protein | 294 | 61% 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 | Nuclear mRNA export protein SAC3 | protein | 17 | 88% helix, 0% strand | — |
| E | Nuclear mRNA export protein SAC3 | protein | 24 | 88% helix, 0% strand | — |
| F | Nuclear mRNA export protein SAC3 | protein | 11 | 82% helix, 0% strand | — |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.62 | 0.89 | 22 | empty |
| 2 | 340 | 0.60 | 0.77 | 32 | empty |
| 3 | 184 | 0.54 | 0.79 | 28 | empty |
| 4 | 140 | 0.52 | 0.80 | 23 | empty |
| 5 | 262 | 0.52 | 0.75 | 28 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2381 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2372 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 231 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 57 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5G5P · 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 5G5P · PDBe 5G5P · UniProt P46674 · UniProt Q08231 · UniProt O94742
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