MolNFT v1 · #179598 · protein
Cryo-EM structure of the sec complex from T. lanuginosus, wild-type, class with SEC62, plug-open conformation
7KAL · Protein transport channel SEC61 complex, alpha subunit…: “Cryo-EM structure of the sec complex from T. lanuginosus, wild-type, class with SEC62, plug-open conformation”. Electron microscopy, 20 pockets (best druggability 0.73).…
- PDB
- 7KAL
- Type
- protein
- Length
- 1,429 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 0.73
Structure
electron microscopy · 7 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport channel SEC61 complex, alpha subunit (SEC61) | protein | 437 | 62% helix, 6% 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 | 475 | 44% helix, 11% strand | — |
| E | Protein transport protein SEC66/SEC71 | protein | 172 | 84% helix, 0% strand | — |
| F | Protein transport protein SEC72 | protein | 194 | 68% helix, 4% strand | — |
| G | Protein transport protein SEC62 | protein | 62 | 87% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.73 | 0.76 | 101 | empty |
| 2 | 425 | 0.64 | 0.77 | 41 | empty |
| 3 | 642 | 0.63 | 0.74 | 61 | empty |
| 4 | 325 | 0.60 | 0.78 | 41 | empty |
| 5 | 379 | 0.57 | 0.75 | 50 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2086 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1732 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1317 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 937 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 784 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7KAL · 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 7KAL · PDBe 7KAL
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