Research workbench
Closed and deep-inactivated conformation of kcsa-T75A mutant
Analyse Closed and deep-inactivated conformation of kcsa-T75A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BY2
- 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
- P0A333
- Ligands
- F09, DGA, K
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody heavy chain | protein | 219 | 3% helix, 50% strand | — |
| B | Antibody light chain | protein | 212 | 7% helix, 50% strand | — |
| C | PH-gated potassium channel kcsa | protein | 103 | 75% helix, 0% strand | P0A333 |
Ligands and binding sites
- F09 · Nonan-1-ol · ligand · chains A, C
- DGA · Diacyl glycerol · ligand · chains C
- K · Potassium ion · metal · 3 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 | 705 | 0.68 | 0.76 | 55 | empty |
| 2 | 76 | 0.51 | 0.85 | 17 | empty |
| 3 | 123 | 0.43 | 0.76 | 20 | empty |
| 4 | 68 | 0.40 | 0.80 | 22 | empty |
| 5 | 70 | 0.31 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1836 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6BY2 · Closed and deep-inactivated conformation of KcsA-T75A mutant · the same entry in another collection · chain C against C, TM-score 1.00
- P0A333 · AlphaFold monomer V2.0 prediction for pH-gated potassium channel kcsa (P0A333) · 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 P0A333
- Elsewhere: RCSB PDB 6BY2 · PDBe 6BY2 · UniProt P0A333
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