MolNFT v1 · #38766 · protein
Structure of a K channel with an amide to ester substitution in the selectivity filter
2H8P · Fab heavy chain: “Structure of a K channel with an amide to ester substitution in the selectivity filter”. X-ray diffraction, 3 ligands (GOA, B3H, K), 5 pockets (best druggability 0.70). MolNFT v1 #38766 on GenesisL1: 3D structure…
- PDB
- 2H8P
- Type
- protein
- Length
- 531 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
- P0A334
- Ligands
- GOA, B3H, K
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab heavy chain | protein | 219 | 4% helix, 50% strand | — |
| B | Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| C | Kcsa channel | protein | 57 | 70% helix, 0% strand | P0A334 |
| D | Kcsa channel | protein | 43 | 77% helix, 0% strand | — |
Ligands and binding sites
- GOA · Glycolic acid · ligand · chains C, D
- B3H · (2S)-2-(butyryloxy)-3-hydroxypropyl nonanoate · ligand · chains D
- K · Potassium ion · metal · 6 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.70 | 0.76 | 64 | empty |
| 2 | 232 | 0.53 | 0.77 | 46 | empty |
| 3 | 57 | 0.52 | 0.87 | 15 | empty |
| 4 | 79 | 0.51 | 0.84 | 16 | empty |
| 5 | 93 | 0.37 | 0.75 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1888 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1088 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2H8P · Structure 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
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 2H8P · PDBe 2H8P · UniProt P0A334
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