Research workbench
Crystal structure of the GLUK3 ligand binding domain complex with glutamate and zinc: P21212 form
Analyse Crystal structure of the GLUK3 ligand binding domain complex with glutamate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U94
- Type
- protein
- Length
- 1,014 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 3
- UniProt
- P42264
- Ligands
- GLU, ZN, SO4, CL
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 3 | protein | 254 | 38% helix, 22% strand | P42264 |
| B | Glutamate receptor, ionotropic kainate 3 | protein | 253 | 37% helix, 22% strand | P42264 |
| C | Glutamate receptor, ionotropic kainate 3 | protein | 253 | 37% helix, 22% strand | P42264 |
| D | Glutamate receptor, ionotropic kainate 3 | protein | 254 | 37% helix, 21% strand | P42264 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 13 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.82 | 0.86 | 74 | ZN |
| 2 | 66 | 0.71 | 0.97 | 18 | GLU |
| 3 | 58 | 0.70 | 0.98 | 18 | GLU |
| 4 | 57 | 0.70 | 0.97 | 17 | GLU |
| 5 | 61 | 0.70 | 0.97 | 19 | GLU |
Interfaces
6 interfaces between chains.
- A–B · 541 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 316 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 278 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3U94 · Crystal structure of the GluK3 ligand binding domain complex with glutamate and zinc… · the same entry in another collection · chain D against D, TM-score 1.00
- P42264 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 3 (P42264) · 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 P42264
- Elsewhere: RCSB PDB 3U94 · PDBe 3U94 · UniProt P42264
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