MolNFT v1 · #120705 · protein
Structure of the human GLUA2 lbd in complex with GNE3419
5H8S · Glutamate receptor 2,GLUTAMATE receptor 2: “Structure of the human GLUA2 lbd in complex with GNE3419”. X-ray diffraction, 3 ligands (GLU, 5YC, ZN), 7 pockets (best druggability 0.78). MolNFT v1 #120705 on GenesisL1: 3D structure…
- PDB
- 5H8S
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2,GLUTAMATE receptor 2
- UniProt
- P42262
- Ligands
- GLU, 5YC, ZN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 259 | 38% helix, 21% strand | P42262 |
| C | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 262 | 36% helix, 21% strand | P42262 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, C, B
- 5YC · 7-[[ethyl(phenyl)amino]methyl]-2-methyl-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one · ligand · 2 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, C, B
- CAC · Cacodylate ion · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.78 | 0.81 | 117 | 5YC |
| 2 | 688 | 0.72 | 0.78 | 65 | empty |
| 3 | 267 | 0.58 | 0.79 | 31 | empty |
| 4 | 122 | 0.46 | 0.78 | 23 | empty |
| 5 | 115 | 0.40 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 922 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 P42262
- Elsewhere: RCSB PDB 5H8S · PDBe 5H8S · UniProt P42262
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