MolNFT v1 · #128025 · protein
Structure of GLUK1 ligand-binding domain (S1S2) in complex with lm-12B at 2.05 a resolution
5NEB · Glutamate receptor ionotropic, kainate 1: “Structure of GLUK1 ligand-binding domain (S1S2) in complex with lm-12B at 2.05 a resolution”. X-ray diffraction, 3 ligands (8VE, SO4, CL), 7 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 5NEB
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 1
- UniProt
- P22756
- Ligands
- 8VE, SO4, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glutamate receptor ionotropic, kainate 1 | protein | 251 | 40% helix, 24% strand | P22756 |
| A | Glutamate receptor ionotropic, kainate 1 | protein | 256 | 39% helix, 23% strand | P22756 |
Ligands and binding sites
- 8VE · (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 8 copies · chains B, A
- CL · Chloride ion · ion · 4 copies · chains B, A
- GOL · Glycerol · additive · 2 copies · chains B, A
- ACT · Acetate ion · additive · chains B
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 | 879 | 0.76 | 0.79 | 87 | CL, GOL, SO4 |
| 2 | 92 | 0.75 | 0.97 | 25 | 8VE |
| 3 | 118 | 0.73 | 0.93 | 29 | 8VE |
| 4 | 108 | 0.50 | 0.81 | 24 | GOL |
| 5 | 67 | 0.42 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 850 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NEB · Structure of GluK1 ligand-binding domain (S1S2) in complex with LM-12b at 2.05 A… · the same entry in another collection · chain B against B, 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 P22756
- Elsewhere: RCSB PDB 5NEB · PDBe 5NEB · UniProt P22756
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