Research workbench
X-ray structure of a voltage-dependent potassium channel in complex with an Fab
Analyse X-ray structure of a voltage-dependent potassium channel in complex with an Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ORQ
- Type
- protein
- Length
- 657 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6E1 Fab light chain; 6E1 Fab heavy chain; Potassium channel
- UniProt
- P01837, P01865, Q9YDF8
- Ligands
- CD, K
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6E1 Fab light chain | protein | 215 | 7% helix, 47% strand | P01837 |
| B | 6E1 Fab heavy chain | protein | 219 | 5% helix, 48% strand | P01865 |
| C | Potassium channel | protein | 223 | 75% helix, 0% strand | Q9YDF8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.59 | 0.74 | 53 | empty |
| 2 | 136 | 0.54 | 0.81 | 21 | empty |
| 3 | 103 | 0.36 | 0.74 | 20 | empty |
| 4 | 94 | 0.35 | 0.74 | 20 | empty |
| 5 | 67 | 0.35 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2029 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 696 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 91 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1ORQ · X-ray structure of a voltage-dependent potassium channel in complex with an Fab · the same entry in another collection · chain A against A, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain B against A, TM-score 0.52
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain A against A, TM-score 0.49
- Q9YDF8 · AlphaFold monomer V2.0 prediction for voltage-gated potassium channel (Q9YDF8) · a predicted model of the same protein · chain C against A, TM-score 0.37
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 P01837
- Every structure of UniProt P01865
- Every structure of UniProt Q9YDF8
- Elsewhere: RCSB PDB 1ORQ · PDBe 1ORQ · UniProt P01837 · UniProt P01865 · UniProt Q9YDF8
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