Research workbench
Cryo-EM structure of C9ORF72-SMCR8-WDR41
Analyse Cryo-EM structure of C9ORF72-SMCR8-WDR41 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LT0
- Type
- protein
- Length
- 2,228 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 41; Guanine nucleotide exchange protein SMCR8; Guanine…
- UniProt
- Q9HAD4, Q8TEV9, Q96LT7
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Wd repeat-containing protein 41 | protein | 343 | 3% helix, 38% strand | Q9HAD4 |
| B, E | Guanine nucleotide exchange protein SMCR8 | protein | 386 | 44% helix, 11% strand | Q8TEV9 |
| C, F | Guanine nucleotide exchange C9ORF72 | protein | 385 | 44% helix, 12% strand | Q96LT7 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.81 | 0.82 | 91 | empty |
| 2 | 1024 | 0.80 | 0.81 | 116 | empty |
| 3 | 861 | 0.80 | 0.82 | 84 | empty |
| 4 | 973 | 0.77 | 0.79 | 98 | empty |
| 5 | 78 | 0.71 | 0.95 | 26 | empty |
Interfaces
9 interfaces between chains.
- B–C · 2650 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2642 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1596 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1595 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 404 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6LT0 · cryo-EM structure of C9ORF72-SMCR8-WDR41 · the same entry in another collection · chain F against F, TM-score 1.00
- Q96LT7 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange C9ORF72 (Q96LT7) · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q9HAD4 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 41 (Q9HAD4) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q8TEV9 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange protein SMCR8 (Q8TEV9) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q9HAD4
- Every structure of UniProt Q8TEV9
- Every structure of UniProt Q96LT7
- Elsewhere: RCSB PDB 6LT0 · PDBe 6LT0 · UniProt Q9HAD4 · UniProt Q8TEV9 · UniProt Q96LT7
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