Research workbench
Crystal structure of the mthk rck in complex with cadmium
Analyse Crystal structure of the mthk rck in complex with cadmium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KXD
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-gated potassium channel mthk
- UniProt
- O27564
- Ligands
- CD
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calcium-gated potassium channel mthk | protein | 224 | 39% helix, 23% strand | O27564 |
| B | Calcium-gated potassium channel mthk | protein | 219 | 39% helix, 23% strand | O27564 |
Ligands and binding sites
- CD · Cadmium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.67 | 0.79 | 36 | CD |
| 2 | 259 | 0.54 | 0.76 | 48 | CD |
| 3 | 112 | 0.47 | 0.79 | 17 | empty |
| 4 | 182 | 0.46 | 0.75 | 20 | empty |
| 5 | 183 | 0.45 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3368 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3KXD · Crystal structure of the mthk rck in complex with cadmium · the same entry in another collection · chain A against A, TM-score 1.00
- O27564 · AlphaFold monomer V2.0 prediction for calcium-gated potassium channel mthk (O27564) · a predicted model of the same protein · chain B 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 O27564
- Elsewhere: RCSB PDB 3KXD · PDBe 3KXD · UniProt O27564
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