Research workbench
Structure of human KV1.3 with A0194009G09 nanobodies (alternate conformation)
Analyse Structure of human KV1.3 with A0194009G09 nanobodies (alternate conformation) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DFL
- Type
- protein
- Length
- 1,908 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium voltage-gated channel subfamily a member 3,GREEN fluorescent protein fusion…
- UniProt
- P22001
- Ligands
- K
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Potassium voltage-gated channel subfamily a member 3,GREEN fluorescent protein fusion | protein | 362 | 57% helix, 5% strand | P22001 |
| E, F, G, H | Nanobody A0194009G09 | protein | 115 | 3% helix, 55% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.83 | 0.84 | 88 | empty |
| 2 | 1003 | 0.80 | 0.81 | 48 | empty |
| 3 | 560 | 0.66 | 0.76 | 51 | empty |
| 4 | 551 | 0.65 | 0.76 | 53 | empty |
| 5 | 52 | 0.65 | 0.94 | 18 | empty |
Interfaces
14 interfaces between chains.
- A–D · 2354 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2353 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2343 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2331 Ų buried · 13 hydrogen bonds · protein-protein
- G–D · 583 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 8DFL · Structure of human Kv1.3 with A0194009G09 nanobodies (alternate conformation) · the same entry in another collection · chain D against D, TM-score 1.00
- P22001 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily a member… · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P22001
- Elsewhere: RCSB PDB 8DFL · PDBe 8DFL · UniProt P22001
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.