Research workbench
Cryo-EM structure of the sec complex from S. cerevisiae, SEC63 FN3 mutant, class with SEC62
Analyse Cryo-EM structure of the sec complex from S. cerevisiae, SEC63 FN3 mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KAS
- Type
- protein
- Length
- 1,385 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC61; Protein transport protein SSS1; Protein transport…
- UniProt
- P32915, P35179, P52870, P14906, P33754, P39742
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 | protein | 430 | 60% helix, 7% strand | P32915 |
| C | Protein transport protein SSS1 | protein | 55 | 85% helix, 0% strand | P35179 |
| B | Protein transport protein SBH1 | protein | 32 | 88% helix, 3% strand | P52870 |
| D | Protein translocation protein SEC63 | protein | 484 | 44% helix, 10% strand | P14906 |
| E | Translocation protein SEC66 | protein | 138 | 80% helix, 1% strand | P33754 |
| F | Translocation protein SEC72 | protein | 190 | 67% helix, 3% strand | P39742 |
| G | Protein transport protein SEC62 | protein | 56 | 86% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.83 | 0.84 | 75 | empty |
| 2 | 266 | 0.59 | 0.78 | 27 | empty |
| 3 | 171 | 0.57 | 0.81 | 19 | empty |
| 4 | 273 | 0.57 | 0.77 | 45 | empty |
| 5 | 241 | 0.57 | 0.78 | 33 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2223 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1840 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1242 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1057 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KAS · Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class with… · the same entry in another collection · chain G against G, TM-score 1.00
- 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 0.90
- 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 0.88
- 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 0.83
- P39742 · AlphaFold monomer V2.0 prediction for translocation protein SEC72 (P39742) · a predicted model of the same protein · chain F against A, TM-score 0.80
- P33754 · AlphaFold monomer V2.0 prediction for translocation protein SEC66 (P33754) · a predicted model of the same protein · chain E against A, TM-score 0.80
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 P35179
- Every structure of UniProt P52870
- Every structure of UniProt P14906
- Every structure of UniProt P33754
- Every structure of UniProt P39742
- Elsewhere: RCSB PDB 7KAS · PDBe 7KAS · UniProt P32915 · UniProt P35179 · UniProt P52870 · UniProt P14906 · UniProt P33754 · UniProt P39742
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