Research workbench
Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide
Analyse Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S1X
- Type
- protein
- Length
- 1,742 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Solute carrier family 12 member 2
- UniProt
- P55011
- Ligands
- 82U, K, CL
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Solute carrier family 12 member 2 | protein | 871 | 56% helix, 7% strand | P55011 |
Ligands and binding sites
- 82U · 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid · ligand · 2 copies · chains B, A
- K · Potassium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.76 | 0.83 | 52 | empty |
| 2 | 542 | 0.75 | 0.82 | 52 | empty |
| 3 | 391 | 0.71 | 0.83 | 44 | 82U |
| 4 | 437 | 0.71 | 0.81 | 51 | 82U |
| 5 | 101 | 0.55 | 0.84 | 24 | empty |
Interfaces
1 interface between chains.
- B–A · 6011 Ų buried · 90 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7S1X · Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.89
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 7S1X · PDBe 7S1X · UniProt P55011
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