Research workbench
Structure of Contracted C. elegans TMC-1 complex
Analyse Structure of Contracted C. elegans TMC-1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7USX
- Type
- protein
- Length
- 1,670 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.09
- Source
- Caenorhabditis elegans
- Molecule
- Transmembrane channel-like protein 1; CALMyrin (Calcium and Integrin Binding protein)…
- UniProt
- D3KZG3, Q93640, Q9XXE7
- Ligands
- D12, R16, PLM, PEE, CLR, 3PE, NAG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.09 · 3 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transmembrane channel-like protein 1 | protein | 605 | 69% helix, 0% strand | D3KZG3 |
| C, E | CALMyrin (Calcium and Integrin Binding protein) homolog | protein | 184 | 57% helix, 4% strand | Q93640 |
| D, F | Transmembrane inner ear expressed protein | protein | 46 | 61% helix, 0% strand | Q9XXE7 |
Ligands and binding sites
- D12 · Dodecane · ligand · 28 copies · chains A, B, D, F
- R16 · Hexadecane · ligand · 8 copies · chains A, B
- PLM · Palmitic acid · ligand · 4 copies · chains A, D, B, F
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, C, B, E
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, D, B, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.84 | 0.85 | 106 | CA |
| 2 | 986 | 0.84 | 0.85 | 101 | CA, PEE |
| 3 | 292 | 0.75 | 0.87 | 44 | empty |
| 4 | 71 | 0.74 | 0.98 | 20 | empty |
| 5 | 63 | 0.72 | 0.97 | 17 | empty |
Interfaces
7 interfaces between chains.
- B–E · 3173 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 3159 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1559 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 806 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 805 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 lipid, 2 disulfide, 2 glycan (palmitoylation, disulfide, N-glycosylation).
Compared structures
- D3KZG3 · AlphaFold monomer V2.0 prediction for transmembrane channel-like protein 1 (D3KZG3) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 D3KZG3
- Every structure of UniProt Q93640
- Every structure of UniProt Q9XXE7
- Elsewhere: RCSB PDB 7USX · PDBe 7USX · UniProt D3KZG3 · UniProt Q93640 · UniProt Q9XXE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.