MolNFT v1 · #124951 · protein
GLUK2EM with LY466195
5KUH · Glutamate receptor ionotropic, kainate 2: “GLUK2EM with LY466195”. Electron microscopy, 1 ligand (LY5), 20 pockets (best druggability 0.83). MolNFT v1 #124951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KUH
- Type
- protein
- Length
- 2,544 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 2
- UniProt
- P42260
- Ligands
- LY5
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate receptor ionotropic, kainate 2 | protein | 636 | 37% helix, 24% strand | P42260 |
Ligands and binding sites
- LY5 · (3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid · ligand · 4 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.83 | 0.87 | 128 | empty |
| 2 | 674 | 0.82 | 0.87 | 125 | empty |
| 3 | 979 | 0.82 | 0.83 | 149 | empty |
| 4 | 533 | 0.81 | 0.88 | 99 | empty |
| 5 | 530 | 0.81 | 0.87 | 93 | empty |
Interfaces
5 interfaces between chains.
- C–D · 538 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 228 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KUH · GluK2EM with LY466195 · the same entry in another collection · chain D against D, TM-score 1.00
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 P42260
- Elsewhere: RCSB PDB 5KUH · PDBe 5KUH · UniProt P42260
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