Research workbench
Crystal structures of the single PDZ domains from GRASP65 and their interaction with the golgin GM130
Analyse Crystal structures of the single PDZ domains from GRASP65 and their interaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G8W
- Type
- protein
- Length
- 179 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Golgi reassembly-stacking protein 1
- UniProt
- Q9BQQ3
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Golgi reassembly-stacking protein 1 | protein | 92 | 12% helix, 34% strand | Q9BQQ3 |
| B | Golgi reassembly-stacking protein 1 | protein | 87 | 14% helix, 34% strand | Q9BQQ3 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.45 | 0.77 | 22 | empty |
| 2 | 53 | 0.36 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6G8W · Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BQQ3 · AlphaFold monomer V2.0 prediction for golgi reassembly-stacking protein 1 (Q9BQQ3) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q9BQQ3
- Elsewhere: RCSB PDB 6G8W · PDBe 6G8W · UniProt Q9BQQ3
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