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Cryo-EM structure of the sec complex from T. lanuginosus, wild-type, class with SEC62, plug-closed conformation
Analyse Cryo-EM structure of the sec complex from T. lanuginosus, 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
- 7KAM
- Type
- protein
- Length
- 1,445 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport channel SEC61 complex, alpha subunit (SEC61); Protein transport channel…
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 7 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport channel SEC61 complex, alpha subunit (SEC61) | protein | 452 | 59% helix, 6% strand | — |
| C | Protein transport channel SEC61 complex, gamma subunit (SSS1) | protein | 57 | 84% helix, 2% strand | — |
| B | Protein transport channel SEC61 complex, beta subunit (SBH1) | protein | 32 | 84% helix, 6% strand | — |
| D | Protein transport protein SEC63 | protein | 476 | 43% helix, 10% strand | — |
| E | Protein transport protein SEC66/SEC71 | protein | 172 | 83% helix, 0% strand | — |
| F | Protein transport protein SEC72 | protein | 194 | 68% helix, 2% strand | — |
| G | Protein transport protein SEC62 | protein | 62 | 87% 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 | 922 | 0.76 | 0.79 | 95 | empty |
| 2 | 1090 | 0.71 | 0.75 | 110 | empty |
| 3 | 723 | 0.68 | 0.76 | 81 | empty |
| 4 | 400 | 0.63 | 0.77 | 42 | empty |
| 5 | 361 | 0.62 | 0.77 | 39 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2143 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1698 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1315 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 909 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 846 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7KAM · Cryo-EM structure of the Sec complex from T. lanuginosus, wild-type, class with Sec62… · 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 7KAM · PDBe 7KAM
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