Research workbench
Structure of the clc-EC1 deltanc construct in 100MM fluoride
Analyse Structure of the clc-EC1 deltanc construct in 100MM fluoride in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KJQ
- Type
- protein
- Length
- 1,749 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H(+)/CL(-) exchange transporter clca; Fab, heavy chain; Fab, light chain
- UniProt
- P37019
- Ligands
- F
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H(+)/CL(-) exchange transporter clca | protein | 444 | 77% helix, 1% strand | P37019 |
| B | H(+)/CL(-) exchange transporter clca | protein | 441 | 76% helix, 0% strand | P37019 |
| C, E | Fab, heavy chain | protein | 221 | 4% helix, 51% strand | — |
| D, F | Fab, light chain | protein | 211 | 4% helix, 50% strand | — |
Ligands and binding sites
- F · Fluoride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.81 | 0.87 | 52 | empty |
| 2 | 584 | 0.76 | 0.82 | 65 | empty |
| 3 | 549 | 0.74 | 0.82 | 64 | empty |
| 4 | 336 | 0.67 | 0.82 | 31 | empty |
| 5 | 315 | 0.67 | 0.82 | 28 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3571 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1924 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1914 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 517 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 463 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4KJQ · Structure of the CLC-ec1 deltaNC construct in 100mM fluoride · the same entry in another collection · chain F against F, TM-score 1.00
- P37019 · AlphaFold monomer V2.0 prediction for H(+)/CL(-) exchange transporter clca (P37019) · a predicted model of the same protein · chain B 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 P37019
- Elsewhere: RCSB PDB 4KJQ · PDBe 4KJQ · UniProt P37019
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