Research workbench
Open conformation of KcsA deep-inactivated
Analyse Open conformation of KcsA deep-inactivated in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VKE
- Type
- protein
- Length
- 527 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.37
- Source
- Mus musculus; Streptomyces lividans
- Molecule
- Antibody Light Chain; Antibody Heavy Chain; pH-gated potassium channel KcsA
- UniProt
- P0A334
- Ligands
- F09, 1EM, K
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.37 · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Light Chain | protein | 219 | 4% helix, 49% strand | — |
| B | Antibody Heavy Chain | protein | 212 | 5% helix, 47% strand | — |
| C | pH-gated potassium channel KcsA | protein | 96 | 73% 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 · 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 | 707 | 0.68 | 0.76 | 60 | empty |
| 2 | 63 | 0.51 | 0.85 | 17 | empty |
| 3 | 69 | 0.49 | 0.85 | 17 | empty |
| 4 | 191 | 0.48 | 0.75 | 31 | empty |
| 5 | 95 | 0.35 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1820 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 430 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 5VKE · PDBe 5VKE · UniProt P0A334
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