MolNFT v1 · #90240 · protein
Crystal structure of the GRASP55 grasp domain with a phosphomimetic mutation (S189D)
4EDJ · Golgi reassembly-stacking protein 2: “Crystal structure of the GRASP55 grasp domain with a phosphomimetic mutation (S189D)”. X-ray diffraction, 1 ligand (K), 6 pockets (best druggability 0.79). MolNFT v1 #90240 on GenesisL1: 3D…
- PDB
- 4EDJ
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Golgi reassembly-stacking protein 2
- UniProt
- Q9H8Y8
- Ligands
- K
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Golgi reassembly-stacking protein 2 | protein | 205 | 15% helix, 32% strand | Q9H8Y8 |
| B | Golgi reassembly-stacking protein 2 | protein | 203 | 16% helix, 33% strand | Q9H8Y8 |
Ligands and binding sites
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.79 | 0.80 | 99 | empty |
| 2 | 164 | 0.66 | 0.86 | 34 | empty |
| 3 | 97 | 0.46 | 0.80 | 22 | empty |
| 4 | 52 | 0.29 | 0.75 | 12 | empty |
| 5 | 53 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1111 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4EDJ · Crystal structure of the GRASP55 GRASP Domain with a phosphomimetic mutation (S189D) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H8Y8 · AlphaFold monomer V2.0 prediction for golgi reassembly-stacking protein 2 (Q9H8Y8) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q9H8Y8
- Elsewhere: RCSB PDB 4EDJ · PDBe 4EDJ · UniProt Q9H8Y8
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