Research workbench
Structure of a complex of the golgin-245 grip domain with ARL1
Analyse Structure of a complex of the golgin-245 grip domain with ARL1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UPT
- Type
- protein
- Length
- 887 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 1; Golgi autoantigen, golgin subfamily a member 4
- UniProt
- P40616, Q13439
- Ligands
- GTP, MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor-like protein 1 | protein | 169 | 35% helix, 24% strand | P40616 |
| B | Golgi autoantigen, golgin subfamily a member 4 | protein | 58 | 78% helix, 0% strand | Q13439 |
| C | ADP-ribosylation factor-like protein 1 | protein | 163 | 32% helix, 23% strand | P40616 |
| D | Golgi autoantigen, golgin subfamily a member 4 | protein | 52 | 71% helix, 0% strand | Q13439 |
| E | ADP-ribosylation factor-like protein 1 | protein | 168 | 35% helix, 24% strand | P40616 |
| F | Golgi autoantigen, golgin subfamily a member 4 | protein | 56 | 77% helix, 0% strand | Q13439 |
| G | ADP-ribosylation factor-like protein 1 | protein | 170 | 35% helix, 25% strand | P40616 |
| H | Golgi autoantigen, golgin subfamily a member 4 | protein | 51 | 75% helix, 0% strand | Q13439 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.73 | 0.76 | 100 | GTP, MG |
| 2 | 180 | 0.50 | 0.77 | 30 | empty |
| 3 | 143 | 0.50 | 0.79 | 16 | empty |
| 4 | 92 | 0.42 | 0.78 | 24 | GTP, MG |
| 5 | 67 | 0.36 | 0.78 | 20 | GTP, MG |
Interfaces
10 interfaces between chains.
- F–H · 1170 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 1159 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 718 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 686 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 673 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 1UPT · Structure of a complex of the golgin-245 GRIP domain with Arl1 · the same entry in another collection · chain H against H, TM-score 1.00
- P40616 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 1 (P40616) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P40616
- Every structure of UniProt Q13439
- Elsewhere: RCSB PDB 1UPT · PDBe 1UPT · UniProt P40616 · UniProt Q13439
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