Research workbench
Cryo-EM structure of human NKCC1 (TM domain)
Analyse Cryo-EM structure of human 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
- 7ZGO
- Type
- protein
- Length
- 940 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Homo sapiens
- Molecule
- Solute carrier family 12 member 2
- UniProt
- P55011
- Ligands
- POV, Y01, NA, K, CL
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · resolution 2.55 · 1 distinct chain · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Solute carrier family 12 member 2 | protein | 470 | 71% helix, 1% strand | P55011 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 7 copies · chains A, B
- Y01 · Cholesterol hemisuccinate · ligand · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 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
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.83 | 0.85 | 57 | POV |
| 2 | 314 | 0.62 | 0.79 | 41 | empty |
| 3 | 321 | 0.61 | 0.79 | 40 | empty |
| 4 | 138 | 0.48 | 0.78 | 35 | empty |
| 5 | 117 | 0.47 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- P55011 · AlphaFold monomer V2.0 prediction for solute carrier family 12 member 2 (P55011) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P55011
- Elsewhere: RCSB PDB 7ZGO · PDBe 7ZGO · UniProt P55011
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