Research workbench
Structure of NKCC1 TM domain
Analyse Structure of NKCC1 TM domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NPH
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Danio rerio
- Molecule
- Solute carrier family 12 (sodium/potassium/chloride transporter), member 2
- UniProt
- A0A0G2KGS0
- Ligands
- POV, K, CL
- Pockets
- 10 · best druggability 0.83
Structure
electron microscopy · resolution 2.9 · 1 distinct chain · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Solute carrier family 12 (sodium/potassium/chloride transporter), member 2 | protein | 472 | 62% helix, 1% strand | A0A0G2KGS0 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 7 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.83 | 0.84 | 61 | POV |
| 2 | 427 | 0.68 | 0.80 | 62 | CL |
| 3 | 425 | 0.67 | 0.80 | 57 | CL |
| 4 | 124 | 0.46 | 0.77 | 30 | empty |
| 5 | 83 | 0.42 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 635 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6NPH · Structure of NKCC1 tm domain · 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 A0A0G2KGS0
- Elsewhere: RCSB PDB 6NPH · PDBe 6NPH · UniProt A0A0G2KGS0
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