Research workbench
Crystal structure of the clc chloride channel from S. typhimurium
Analyse Crystal structure of the clc chloride channel from S. typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KPL
- Type
- protein
- Length
- 1,762 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative clc family, chlorine transport protein
- UniProt
- Q8ZRP8
- Ligands
- MYS, CL, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative clc family, chlorine transport protein | protein | 430 | 77% helix, 1% strand | Q8ZRP8 |
| B, D | Putative clc family, chlorine transport protein | protein | 451 | 76% helix, 1% strand | Q8ZRP8 |
Ligands and binding sites
- MYS · Pentadecane · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, C
- OCT · N-octane · additive · 2 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.81 | 0.86 | 48 | empty |
| 2 | 1113 | 0.76 | 0.78 | 104 | SO4, MYS |
| 3 | 341 | 0.73 | 0.85 | 30 | empty |
| 4 | 443 | 0.71 | 0.82 | 58 | empty |
| 5 | 329 | 0.71 | 0.84 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2886 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2881 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1230 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 392 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 360 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1KPL · Crystal Structure of the ClC Chloride Channel from S. typhimurium · the same entry in another collection · chain D against D, TM-score 1.00
- Q8ZRP8 · AlphaFold monomer V2.0 prediction for H(+)/CL(-) exchange transporter clca (Q8ZRP8) · 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 Q8ZRP8
- Elsewhere: RCSB PDB 1KPL · PDBe 1KPL · UniProt Q8ZRP8
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