Research workbench
Cryo-EM structure of the signal sequence-engaged post-translational sec translocon
Analyse Cryo-EM structure of the signal sequence-engaged post-translational sec… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AFT
- Type
- protein
- Length
- 1,353 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC61; Protein transport protein SBH1; Protein transport…
- UniProt
- P32915, P52870, P35179, P14906, P33754, P39742, P21825, P01149
- Pockets
- 16 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 | protein | 391 | 64% helix, 5% strand | P32915 |
| B | Protein transport protein SBH1 | protein | 32 | 84% helix, 3% strand | P52870 |
| C | Protein transport protein SSS1 | protein | 55 | 82% helix, 0% strand | P35179 |
| D | Protein translocation protein SEC63 | protein | 487 | 44% helix, 12% strand | P14906 |
| E | Translocation protein SEC66 | protein | 135 | 78% helix, 0% strand | P33754 |
| F | Translocation protein SEC72 | protein | 190 | 69% helix, 1% strand | P39742 |
| G | Translocation protein SEC62,TRANSLOCATION protein SEC62 | protein | 50 | 90% helix, 0% strand | P21825 |
| H | Mating factor alpha-1,MATING factor alpha-1 | protein | 13 | 62% helix, 0% strand | P01149 |
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.82 | 0.84 | 127 | empty |
| 2 | 433 | 0.72 | 0.83 | 83 | empty |
| 3 | 562 | 0.71 | 0.80 | 94 | empty |
| 4 | 982 | 0.69 | 0.74 | 105 | empty |
| 5 | 174 | 0.58 | 0.81 | 36 | empty |
Interfaces
12 interfaces between chains.
- A–D · 406 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 389 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 316 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 160 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7AFT · Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon · the same entry in another collection · chain H against H, TM-score 1.00
- P14906 · AlphaFold monomer V2.0 prediction for protein translocation protein SEC63 (P14906) · a predicted model of the same protein · chain D against A, TM-score 0.89
- P32915 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 (P32915) · a predicted model of the same protein · chain A against A, TM-score 0.89
- P52870 · AlphaFold monomer V2.0 prediction for protein transport protein SBH1 (P52870) · a predicted model of the same protein · chain B against A, TM-score 0.82
- P33754 · AlphaFold monomer V2.0 prediction for translocation protein SEC66 (P33754) · a predicted model of the same protein · chain E against A, TM-score 0.79
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 P32915
- Every structure of UniProt P52870
- Every structure of UniProt P35179
- Every structure of UniProt P14906
- Every structure of UniProt P33754
- Every structure of UniProt P39742
- Every structure of UniProt P21825
- Every structure of UniProt P01149
- Elsewhere: RCSB PDB 7AFT · PDBe 7AFT · UniProt P32915 · UniProt P52870 · UniProt P35179 · UniProt P14906 · UniProt P33754 · UniProt P39742 · UniProt P21825 · UniProt P01149
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