Research workbench
Cryo-EM structure of the sec complex from T. lanuginosus, SEC62- lacking mutant (delta SEC62)
Analyse Cryo-EM structure of the sec complex from T. lanuginosus, SEC62- lacking mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KAN
- Type
- protein
- Length
- 1,371 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport channel SEC61 complex, alpha subunit (SEC61); Protein transport channel…
- Ligands
- PC1
- Pockets
- 18 · best druggability 0.77
Structure
electron microscopy · 6 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport channel SEC61 complex, alpha subunit (SEC61) | protein | 446 | 62% helix, 7% strand | — |
| C | Protein transport channel SEC61 complex, gamma subunit (SSS1) | protein | 57 | 86% helix, 2% strand | — |
| B | Protein transport channel SEC61 complex, beta subunit (SBH1) | protein | 32 | 84% helix, 6% strand | — |
| D | Protein transport protein SEC63 | protein | 470 | 43% helix, 12% strand | — |
| E | Protein transport protein SEC66/SEC71 | protein | 172 | 81% helix, 0% strand | — |
| F | Protein transport protein SEC72 | protein | 194 | 66% helix, 2% strand | — |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.77 | 0.80 | 114 | empty |
| 2 | 830 | 0.72 | 0.77 | 70 | empty |
| 3 | 844 | 0.69 | 0.75 | 69 | empty |
| 4 | 334 | 0.61 | 0.78 | 46 | empty |
| 5 | 266 | 0.60 | 0.78 | 31 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2162 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1703 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1265 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 960 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 821 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7KAN · Cryo-EM structure of the Sec complex from T. lanuginosus, Sec62-lacking mutant (Delta… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7KAN · PDBe 7KAN
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.