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Crystal structure of the tetramerization domain (29-147) from human voltage-gated potassium channel KV2.1 in C 2 2 21 space group
Analyse Crystal structure of the tetramerization domain (29-147) from human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SPD
- Type
- protein
- Length
- 532 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium voltage-gated channel subfamily B member 1
- UniProt
- Q14721
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Potassium voltage-gated channel subfamily B member 1 | protein | 107 | 38% helix, 20% strand | Q14721 |
| B | Potassium voltage-gated channel subfamily B member 1 | protein | 106 | 39% helix, 20% strand | Q14721 |
| D | Potassium voltage-gated channel subfamily B member 1 | protein | 107 | 36% helix, 20% strand | Q14721 |
| E | Potassium voltage-gated channel subfamily B member 1 | protein | 105 | 33% helix, 20% strand | Q14721 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.46 | 0.76 | 29 | empty |
| 2 | 102 | 0.42 | 0.78 | 17 | empty |
| 3 | 144 | 0.40 | 0.73 | 32 | PEG |
| 4 | 88 | 0.32 | 0.73 | 19 | PEG |
Interfaces
5 interfaces between chains.
- D–E · 776 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 753 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 737 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 724 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 654 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7SPD · Crystal Structure of The Tetramerization Domain (29-147) From Human Voltage-gated… · the same entry in another collection · chain E against E, TM-score 1.00
- Q14721 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily B member… · a predicted model of the same protein · chain E against A, TM-score 0.95
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 Q14721
- Elsewhere: RCSB PDB 7SPD · PDBe 7SPD · UniProt Q14721
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