MolNFT v1 · #137313 · protein
Structure of a mechanotransduction ion channel drosophila nompc in nanodisc
5VKQ · No mechanoreceptor potential C isoform L: “Structure of a mechanotransduction ion channel drosophila nompc in nanodisc”. Electron microscopy, 1 ligand (PCF), 20 pockets (best druggability 0.82). MolNFT v1 #137313 on GenesisL1: 3D…
- PDB
- 5VKQ
- Type
- protein
- Length
- 5,996 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- No mechanoreceptor potential C isoform L
- UniProt
- E0A9E1
- Ligands
- PCF
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 56% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | No mechanoreceptor potential C isoform L | protein | 1499 | 56% helix, 0% strand | E0A9E1 |
Ligands and binding sites
- PCF · 1,2-diacyl-sn-glycero-3-phoshocholine · ligand · 32 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 823 | 0.82 | 0.84 | 88 | empty |
| 2 | 840 | 0.79 | 0.81 | 79 | PCF |
| 3 | 526 | 0.77 | 0.84 | 48 | empty |
| 4 | 521 | 0.76 | 0.83 | 46 | empty |
| 5 | 533 | 0.76 | 0.83 | 47 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3398 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3370 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 3348 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 3334 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VKQ · Structure of a mechanotransduction ion channel Drosophila NOMPC in nanodisc · 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
- Every structure of UniProt E0A9E1
- Elsewhere: RCSB PDB 5VKQ · PDBe 5VKQ · UniProt E0A9E1
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