Research workbench
Crystal structure of kcsa-Fab-tba complex in rb+
Analyse Crystal structure of kcsa-Fab-tba complex in rb+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DWE
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab heavy chain; Antibody Fab light chain; Voltage-gated potassium channel
- UniProt
- P0A334
- Ligands
- L2C, F09, TBA, RB
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab heavy chain | protein | 219 | 5% helix, 49% strand | — |
| B | Antibody Fab light chain | protein | 212 | 6% helix, 51% strand | — |
| C | Voltage-gated potassium channel | protein | 103 | 73% helix, 0% strand | P0A334 |
Ligands and binding sites
- L2C · (2S)-3-hydroxy-2-(nonanoyloxy)propyl laurate · ligand · chains C
- F09 · Nonan-1-ol · ligand · chains A, C
- TBA · Tetrabutylammonium ion · ligand · chains C
- RB · Rubidium ion · metal · 3 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.68 | 0.76 | 57 | empty |
| 2 | 72 | 0.58 | 0.89 | 18 | empty |
| 3 | 51 | 0.51 | 0.88 | 15 | empty |
| 4 | 118 | 0.48 | 0.79 | 20 | empty |
| 5 | 108 | 0.37 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1810 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 482 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2DWE · Crystal structure of KcsA-FAB-TBA complex in Rb+ · 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 P0A334
- Elsewhere: RCSB PDB 2DWE · PDBe 2DWE · UniProt P0A334
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