Research workbench
Crystal structure of gae domain of GGA2P from saccharomyces cerevisiae
Analyse Crystal structure of gae domain of GGA2P from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MNM
- Type
- protein
- Length
- 334 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-binding protein GGA2
- UniProt
- P38817
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor-binding protein GGA2 | protein | 112 | 0% helix, 59% strand | P38817 |
| C | ADP-ribosylation factor-binding protein GGA2 | protein | 110 | 0% helix, 62% strand | P38817 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.63 | 0.94 | 20 | empty |
| 2 | 123 | 0.48 | 0.79 | 25 | GOL |
| 3 | 73 | 0.41 | 0.79 | 17 | GOL |
| 4 | 54 | 0.39 | 0.81 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 661 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 645 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (methylation).
Compared structures
- 3MNM · Crystal structure of GAE domain of GGA2p from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P38817 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-binding protein GGA2… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P38817
- Elsewhere: RCSB PDB 3MNM · PDBe 3MNM · UniProt P38817
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