Research workbench
Cryo-EM structure of the sec complex from yeast, SEC63 FN3 and residues 210-216 mutated
Analyse Cryo-EM structure of the sec complex from yeast, SEC63 FN3 and residues 210-216… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KB5
- Type
- protein
- Length
- 1,252 residues
- Chains
- 6
- 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
- Pockets
- 19 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 | protein | 427 | 67% helix, 5% strand | P32915 |
| B | Protein transport protein SBH1 | protein | 32 | 88% helix, 3% strand | P52870 |
| C | Protein transport protein SSS1 | protein | 55 | 87% helix, 2% strand | P35179 |
| D | Protein translocation protein SEC63 | protein | 410 | 38% helix, 12% strand | P14906 |
| E | Translocation protein SEC66 | protein | 138 | 79% helix, 0% strand | P33754 |
| F | Translocation protein SEC72 | protein | 190 | 64% helix, 2% strand | P39742 |
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.84 | 0.84 | 93 | empty |
| 2 | 413 | 0.72 | 0.82 | 47 | empty |
| 3 | 712 | 0.70 | 0.77 | 52 | empty |
| 4 | 184 | 0.70 | 0.88 | 34 | empty |
| 5 | 212 | 0.64 | 0.83 | 32 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2222 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1891 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1085 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 908 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 609 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7KB5 · Cryo-EM structure of the Sec complex from yeast, Sec63 FN3 and residues 210-216 mutated · 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 0.95
- 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 0.93
- 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 0.69
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
- Elsewhere: RCSB PDB 7KB5 · PDBe 7KB5 · UniProt P32915 · UniProt P52870 · UniProt P35179 · UniProt P14906 · UniProt P33754 · UniProt P39742
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