Research workbench
Cryo-EM structure of the sec complex from S. cerevisiae, SEC61 pore mutant, class with SEC62, conformation 1 (C1)
Analyse Cryo-EM structure of the sec complex from S. cerevisiae, SEC61 pore mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KAP
- Type
- protein
- Length
- 1,398 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 0.84
Structure
electron microscopy · 7 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 | protein | 435 | 62% helix, 7% strand | P32915 |
| C | Protein transport protein SSS1 | protein | 55 | 87% helix, 0% strand | P35179 |
| B | Protein transport protein SBH1 | protein | 32 | 88% helix, 3% strand | P52870 |
| D | Protein translocation protein SEC63 | protein | 492 | 42% helix, 12% strand | P14906 |
| E | Translocation protein SEC66 | protein | 138 | 79% helix, 1% strand | P33754 |
| F | Translocation protein SEC72 | protein | 190 | 67% helix, 2% strand | P39742 |
| G | Protein transport protein SEC62 | protein | 56 | 86% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.84 | 0.85 | 82 | empty |
| 2 | 226 | 0.62 | 0.81 | 27 | empty |
| 3 | 363 | 0.62 | 0.77 | 46 | empty |
| 4 | 484 | 0.61 | 0.75 | 69 | empty |
| 5 | 224 | 0.58 | 0.78 | 22 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2170 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1790 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1508 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1076 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7KAP · Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with… · the same entry in another collection · chain G against G, 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 0.91
- 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 0.87
- 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 0.81
- 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 7KAP · PDBe 7KAP · UniProt P32915 · UniProt P35179 · UniProt P52870 · UniProt P14906 · UniProt P33754 · UniProt P39742
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