Research workbench
Crystal structure of GTP-bound ADP-ribosylation factor like protein 1 (ARL1) and grip domain of GOLGIN245 complex
Analyse Crystal structure of GTP-bound ADP-ribosylation factor like protein 1 (ARL1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R4A
- Type
- protein
- Length
- 864 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
- P61212, Q13439
- Ligands
- GNP, MG
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ADP-ribosylation factor-like protein 1 | protein | 165 | 35% helix, 25% strand | P61212 |
| E, F, G, H | Golgi autoantigen, golgin subfamily a member 4 | protein | 51 | 76% helix, 0% strand | Q13439 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.74 | 0.81 | 56 | empty |
| 2 | 245 | 0.52 | 0.76 | 29 | empty |
| 3 | 89 | 0.43 | 0.79 | 24 | MG, GNP |
| 4 | 85 | 0.42 | 0.79 | 24 | MG, GNP |
| 5 | 75 | 0.41 | 0.80 | 18 | MG, GNP |
Interfaces
10 interfaces between chains.
- E–G · 992 Ų buried · 0 hydrogen bonds · protein-protein
- F–H · 984 Ų buried · 3 hydrogen bonds · protein-protein
- C–G · 710 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 698 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 694 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1R4A · Crystal Structure of GTP-bound ADP-ribosylation Factor Like Protein 1 (Arl1) and GRIP… · the same entry in another collection · chain H against H, TM-score 1.00
- P61212 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 1 (P61212) · a predicted model of the same protein · chain B 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 P61212
- Every structure of UniProt Q13439
- Elsewhere: RCSB PDB 1R4A · PDBe 1R4A · UniProt P61212 · UniProt Q13439
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