MolNFT v1 · #20412 · protein
Structure of ARF1-GDP bound to SEC7 domain complexed with brefeldin a
1RE0 · ADP-ribosylation factor 1: “Structure of ARF1-GDP bound to SEC7 domain complexed with brefeldin a”. X-ray diffraction, 3 ligands (GDP, AFB, MG), 2 pockets (best druggability 0.77). MolNFT v1 #20412 on GenesisL1: 3D structure…
- PDB
- 1RE0
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor 1; Arf guanine-nucleotide exchange factor 1
- UniProt
- P32889, P47102
- Ligands
- GDP, AFB, MG
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor 1 | protein | 162 | 36% helix, 23% strand | P32889 |
| B | Arf guanine-nucleotide exchange factor 1 | protein | 195 | 66% helix, 1% strand | P47102 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- AFB · 1,6,7,8,9,11A,12,13,14,14A-decahydro-1,13-dihydroxy-6-methyl-4H-cyclopent[f]oxacyclotridecin-4-one · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.77 | 0.85 | 51 | MG, AFB |
| 2 | 234 | 0.51 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1480 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1RE0 · Structure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A · the same entry in another collection · chain A against A, TM-score 1.00
- P47102 · AlphaFold monomer V2.0 prediction for arf guanine-nucleotide exchange factor 1 (P47102) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P32889
- Every structure of UniProt P47102
- Elsewhere: RCSB PDB 1RE0 · PDBe 1RE0 · UniProt P32889 · UniProt P47102
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