MolNFT v1 · #122962 · protein
Crystal structure of ARL1-GTP and dcb domain of BIG1 complex
5J5C · ADP-ribosylation factor-like protein 1: “Crystal structure of ARL1-GTP and dcb domain of BIG1 complex”. X-ray diffraction, 3 ligands (GTP, MG, SO4), 6 pockets (best druggability 0.71). MolNFT v1 #122962 on GenesisL1: 3D structure…
- PDB
- 5J5C
- Type
- protein
- Length
- 359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 1; Brefeldin a-inhibited guanine nucleotide-exchange…
- UniProt
- P40616, Q9Y6D6
- Ligands
- GTP, MG, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor-like protein 1 | protein | 165 | 35% helix, 25% strand | P40616 |
| B | Brefeldin a-inhibited guanine nucleotide-exchange protein 1 | protein | 194 | 66% helix, 0% strand | Q9Y6D6 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 555 | 0.71 | 0.80 | 73 | SO4 |
| 2 | 120 | 0.65 | 0.88 | 25 | empty |
| 3 | 84 | 0.44 | 0.80 | 17 | empty |
| 4 | 61 | 0.34 | 0.78 | 16 | MG, GTP |
| 5 | 51 | 0.28 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5J5C · Crystal structure of ARL1-GTP and DCB domain of BIG1 complex · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
- Q9Y6D6 · AlphaFold monomer V2.0 prediction for brefeldin a-inhibited guanine nucleotide-exchange… · a predicted model of the same protein · chain B 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 P40616
- Every structure of UniProt Q9Y6D6
- Elsewhere: RCSB PDB 5J5C · PDBe 5J5C · UniProt P40616 · UniProt Q9Y6D6
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