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Crystal structure of human GGA1 gat domain complexed with the gat- binding domain of RABAPTIN5
Analyse Crystal structure of human GGA1 gat domain complexed with the gat- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X79
- Type
- protein
- Length
- 260 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor binding protein GGA1; Rab GTPase binding effector protein 1
- UniProt
- Q9UJY5, Q15276
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor binding protein GGA1 | protein | 82 | 83% helix, 0% strand | Q9UJY5 |
| B | Rab GTPase binding effector protein 1 | protein | 90 | 97% helix, 0% strand | Q15276 |
| C | Rab GTPase binding effector protein 1 | protein | 88 | 94% helix, 0% strand | Q15276 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains B, C
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 | 60 | 0.34 | 0.77 | 12 | empty |
| 2 | 59 | 0.32 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1018 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 548 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 471 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1X79 · Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJY5 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-binding protein GGA1… · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q15276 · AlphaFold monomer V2.0 prediction for rab GTPase-binding effector protein 1 (Q15276) · a predicted model of the same protein · chain C 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 Q9UJY5
- Every structure of UniProt Q15276
- Elsewhere: RCSB PDB 1X79 · PDBe 1X79 · UniProt Q9UJY5 · UniProt Q15276
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