MolNFT v1 · #117566 · protein
Kcsa with V76ESTER mutation
5EC1 · Antibody Fab fragment light chain: “Kcsa with V76ESTER mutation”. X-ray diffraction, 4 ligands (LHV, F09, DGA), 6 pockets (best druggability 0.67). MolNFT v1 #117566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EC1
- Type
- protein
- Length
- 530 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment light chain; PH-gated potassium channel kcsa
- UniProt
- P0A334
- Ligands
- LHV, F09, DGA, K
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment light chain | protein | 219 | 4% helix, 47% strand | — |
| B | Antibody Fab fragment light chain | protein | 209 | 7% helix, 49% strand | — |
| C | PH-gated potassium channel kcsa | protein | 102 | 72% helix, 0% strand | P0A334 |
Ligands and binding sites
- LHV · (2S)-2-hydroxy-3-methylbutanoic acid · ligand · chains C
- F09 · Nonan-1-ol · ligand · chains A, C
- DGA · Diacyl glycerol · ligand · chains C
- K · Potassium ion · metal · 6 copies · chains C
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 | 647 | 0.67 | 0.76 | 56 | empty |
| 2 | 62 | 0.53 | 0.87 | 16 | empty |
| 3 | 54 | 0.51 | 0.88 | 16 | empty |
| 4 | 128 | 0.42 | 0.76 | 25 | empty |
| 5 | 86 | 0.33 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1823 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 483 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5EC1 · KcsA with V76ester mutation · 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 5EC1 · PDBe 5EC1 · UniProt P0A334
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