Research workbench
Cryo-EM structure of the sec complex from S. cerevisiae, wild-type, class with SEC62, conformation 2 (C2)
Analyse Cryo-EM structure of the sec complex from S. cerevisiae, wild-type, class with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KAJ
- Type
- protein
- Length
- 1,399 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 · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 | protein | 436 | 60% 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, 13% strand | P14906 |
| E | Translocation protein SEC66 | protein | 138 | 78% 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.83 | 0.84 | 75 | empty |
| 2 | 58 | 0.69 | 0.97 | 23 | empty |
| 3 | 308 | 0.64 | 0.80 | 39 | empty |
| 4 | 220 | 0.59 | 0.79 | 22 | empty |
| 5 | 242 | 0.56 | 0.78 | 36 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2180 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1937 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1681 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 995 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KAJ · Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62… · 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 0.90
- 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 0.88
- 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 0.86
- 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 7KAJ · PDBe 7KAJ · UniProt P32915 · UniProt P35179 · UniProt P52870 · UniProt P14906 · UniProt P33754 · UniProt P39742
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