MolNFT v1 · #12031 · protein
Potassium channel kcsa-Fab complex in low concentration of K+
1K4D · Antibody Fab fragment heavy chain: “Potassium channel kcsa-Fab complex in low concentration of K+”. X-ray diffraction, 4 ligands (DGA, F09, K), 6 pockets (best druggability 0.68). MolNFT v1 #12031 on GenesisL1: 3D structure, binding…
- PDB
- 1K4D
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment heavy chain; Antibody Fab fragment light chain; Potassium channel…
- UniProt
- P0A334
- Ligands
- DGA, F09, K, NA
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment heavy chain | protein | 219 | 4% helix, 50% strand | — |
| B | Antibody Fab fragment light chain | protein | 212 | 6% helix, 52% strand | — |
| C | Potassium channel kcsa | protein | 103 | 75% helix, 0% strand | P0A334 |
Ligands and binding sites
- DGA · Diacyl glycerol · ligand · chains C
- F09 · Nonan-1-ol · ligand · chains A, C
- K · Potassium ion · metal · 2 copies · chains C
- NA · Sodium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.68 | 0.76 | 61 | empty |
| 2 | 58 | 0.51 | 0.87 | 20 | empty |
| 3 | 66 | 0.50 | 0.86 | 17 | empty |
| 4 | 149 | 0.47 | 0.77 | 26 | empty |
| 5 | 55 | 0.46 | 0.84 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1830 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 502 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 431 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1K4D · Potassium Channel KcsA-Fab complex in low concentration of K+ · the same entry in another collection · chain A against A, TM-score 1.00
- P0A334 · AlphaFold monomer V2.0 prediction for pH-gated potassium channel kcsa (P0A334) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 1K4D · PDBe 1K4D · UniProt P0A334
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