MolNFT v1 · #179594 · protein
Cryo-EM structure of the sec complex from S. cerevisiae, wild-type, class without SEC62
7KAH · Protein transport protein SEC61: “Cryo-EM structure of the sec complex from S. cerevisiae, wild-type, class without SEC62”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #179594 on GenesisL1: 3D structure…
- PDB
- 7KAH
- Type
- protein
- Length
- 1,349 residues
- Chains
- 6
- 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 · 6 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 | protein | 441 | 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 | 493 | 41% helix, 12% strand | P14906 |
| E | Translocation protein SEC66 | protein | 138 | 80% helix, 1% strand | P33754 |
| F | Translocation protein SEC72 | protein | 190 | 67% helix, 2% strand | P39742 |
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 | 1003 | 0.83 | 0.84 | 71 | empty |
| 2 | 804 | 0.70 | 0.76 | 69 | empty |
| 3 | 58 | 0.68 | 0.96 | 21 | empty |
| 4 | 345 | 0.66 | 0.80 | 38 | empty |
| 5 | 173 | 0.65 | 0.85 | 30 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2188 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1881 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1544 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1051 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KAH · Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class without Sec62 · the same entry in another collection · chain F against F, 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 0.90
- 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
- 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
- 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
- P35179 · AlphaFold monomer V2.0 prediction for protein transport protein SSS1 (P35179) · a predicted model of the same protein · chain C against A, TM-score 0.66
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 7KAH · PDBe 7KAH · UniProt P32915 · UniProt P35179 · UniProt P52870 · UniProt P14906 · UniProt P33754 · UniProt P39742
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