Research workbench
Structure of GLUK1 ligand-binding domain (S1S2) in complex with cip-as at 2.85 a resolution
Analyse Structure of GLUK1 ligand-binding domain (S1S2) in complex with cip-as at 2.85… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NF5
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 1,GLUTAMATE receptor ionotropic, kainate 1
- UniProt
- P22756
- Ligands
- 8VN, CL, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glutamate receptor ionotropic, kainate 1,GLUTAMATE receptor ionotropic, kainate 1 | protein | 255 | 39% helix, 22% strand | P22756 |
| A | Glutamate receptor ionotropic, kainate 1,GLUTAMATE receptor ionotropic, kainate 1 | protein | 254 | 39% helix, 22% strand | P22756 |
Ligands and binding sites
- 8VN · (3~{a}~{S},4~{S},6~{a}~{R})-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-3,4-dicarboxylic acid · ligand · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.77 | 0.81 | 87 | CL |
| 2 | 256 | 0.68 | 0.84 | 32 | 8VN, GOL |
| 3 | 305 | 0.67 | 0.82 | 37 | 8VN, GOL |
| 4 | 175 | 0.60 | 0.82 | 27 | empty |
| 5 | 93 | 0.38 | 0.76 | 16 | GOL |
Interfaces
1 interface between chains.
- B–A · 1136 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5NF5 · Structure of GluK1 ligand-binding domain (S1S2) in complex with CIP-AS at 2.85 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 5NF5 · PDBe 5NF5 · UniProt P22756
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