Research workbench
Cryoem structure of the sec complex from yeast
Analyse Cryoem structure of the sec complex from yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ND1
- Type
- protein
- Length
- 1,179 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC61; Protein translocation protein SEC63; Protein transport…
- UniProt
- P32915, P14906, P35179, P52870, P33754, P39742
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Protein transport protein SEC61 | protein | 390 | 63% helix, 7% strand | P32915 |
| A | Protein translocation protein SEC63 | protein | 461 | 40% helix, 11% strand | P14906 |
| C | Protein transport protein SSS1 | protein | 56 | 80% helix, 0% strand | P35179 |
| D | Protein transport protein SBH1 | protein | 41 | 68% helix, 2% strand | P52870 |
| E | Translocation protein SEC66 | protein | 139 | 80% helix, 0% strand | P33754 |
| F | Translocation protein SEC72 | protein | 92 | 78% helix, 0% strand | P39742 |
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 | 935 | 0.80 | 0.82 | 74 | empty |
| 2 | 987 | 0.77 | 0.79 | 85 | empty |
| 3 | 698 | 0.75 | 0.80 | 57 | empty |
| 4 | 78 | 0.70 | 0.95 | 24 | empty |
| 5 | 417 | 0.58 | 0.74 | 44 | empty |
Interfaces
11 interfaces between chains.
- B–C · 1805 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 1186 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 857 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 716 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 687 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ND1 · CryoEM structure of the Sec Complex from yeast · the same entry in another collection · chain F against F, TM-score 1.00
- P32915 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 (P32915) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P39742 · AlphaFold monomer V2.0 prediction for translocation protein SEC72 (P39742) · a predicted model of the same protein · chain F against A, TM-score 0.93
- P14906 · AlphaFold monomer V2.0 prediction for protein translocation protein SEC63 (P14906) · a predicted model of the same protein · chain A against A, TM-score 0.92
- P33754 · AlphaFold monomer V2.0 prediction for translocation protein SEC66 (P33754) · a predicted model of the same protein · chain E against A, TM-score 0.89
- 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 0.68
- P52870 · AlphaFold monomer V2.0 prediction for protein transport protein SBH1 (P52870) · a predicted model of the same protein · chain D against A, TM-score 0.51
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 P14906
- Every structure of UniProt P35179
- Every structure of UniProt P52870
- Every structure of UniProt P33754
- Every structure of UniProt P39742
- Elsewhere: RCSB PDB 6ND1 · PDBe 6ND1 · UniProt P32915 · UniProt P14906 · UniProt P35179 · UniProt P52870 · UniProt P33754 · UniProt P39742
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