MolNFT v1 · #41278 · protein
Crystal structure of 2ND PDZ domain of glutamate receptor interacting protein-1 (GRIP1)
2JIL: “Crystal structure of 2ND PDZ domain of glutamate receptor interacting protein-1 (GRIP1)”. X-ray diffraction, 1 ligand (SCN), 4 pockets (best druggability 0.46). MolNFT v1 #41278 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2JIL
- Type
- protein
- Length
- 192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor interacting protein-1
- UniProt
- Q9Y3R0
- Ligands
- SCN
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor interacting protein-1 | protein | 95 | 16% helix, 43% strand | Q9Y3R0 |
| B | Glutamate receptor interacting protein-1 | protein | 97 | 19% helix, 45% strand | Q9Y3R0 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.46 | 0.75 | 25 | empty |
| 2 | 83 | 0.35 | 0.75 | 17 | SCN |
| 3 | 62 | 0.33 | 0.77 | 14 | empty |
| 4 | 54 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2JIL · Crystal structure of 2nd PDZ domain of glutamate receptor interacting protein-1 (GRIP1) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y3R0 · AlphaFold monomer V2.0 prediction for glutamate receptor-interacting protein 1 (Q9Y3R0) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9Y3R0
- Elsewhere: RCSB PDB 2JIL · PDBe 2JIL · UniProt Q9Y3R0
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