Research workbench
Closed conformation of kcsa Y82A-F103A mutant
Analyse Closed conformation of kcsa Y82A-F103A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VKH
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody heavy chain; Antibody light chain; PH-gated potassium channel kcsa
- UniProt
- P0A334
- Ligands
- F09, 1EM, K
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody heavy chain | protein | 219 | 5% helix, 48% strand | — |
| B | Antibody light chain | protein | 212 | 6% helix, 52% strand | — |
| C | PH-gated potassium channel kcsa | protein | 103 | 74% helix, 0% strand | P0A334 |
Ligands and binding sites
- F09 · Nonan-1-ol · ligand · chains A, C
- 1EM · (1S)-2-hydroxy-1-[(nonanoyloxy)methyl]ethyl myristate · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.68 | 0.76 | 60 | empty |
| 2 | 146 | 0.51 | 0.80 | 30 | empty |
| 3 | 71 | 0.50 | 0.84 | 15 | empty |
| 4 | 68 | 0.50 | 0.84 | 16 | empty |
| 5 | 57 | 0.48 | 0.86 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1834 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5VKH · Closed conformation of KcsA Y82A-F103A mutant · 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 5VKH · PDBe 5VKH · UniProt P0A334
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