Research workbench
Rb+ complex of a K channel with an amide to ester substitution in the selectivity filter
Analyse Rb+ complex of a K channel with an amide to ester substitution in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HFE
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Kcsa channel
- UniProt
- Q569B4, Q66JS7, P0A333
- Ligands
- GOA, B3H, RB
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab heavy chain | protein | 219 | 4% helix, 48% strand | Q569B4 |
| B | Fab light chain | protein | 211 | 7% helix, 50% strand | Q66JS7 |
| C | Kcsa channel | protein | 57 | 70% helix, 0% strand | P0A333 |
| D | Kcsa channel | protein | 43 | 84% helix, 0% strand | P0A333 |
Ligands and binding sites
- GOA · Glycolic acid · ligand · chains C, D
- B3H · (2S)-2-(butyryloxy)-3-hydroxypropyl nonanoate · ligand · chains D
- RB · Rubidium ion · metal · 5 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 | 804 | 0.70 | 0.76 | 69 | empty |
| 2 | 79 | 0.51 | 0.84 | 16 | empty |
| 3 | 201 | 0.51 | 0.77 | 38 | empty |
| 4 | 59 | 0.49 | 0.86 | 20 | empty |
| 5 | 63 | 0.48 | 0.84 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1882 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1078 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 499 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 440 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2HFE · Rb+ complex of a K channel with an amide to ester substitution in the selectivity filter · the same entry in another collection · chain A against A, 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 Q569B4
- Every structure of UniProt Q66JS7
- Every structure of UniProt P0A333
- Elsewhere: RCSB PDB 2HFE · PDBe 2HFE · UniProt Q569B4 · UniProt Q66JS7 · UniProt P0A333
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