MolNFT v1 · #20246 · protein
Full-length ARF1-GDP-mg in complex with brefeldin a and a SEC7 domain
1R8Q · ADP-ribosylation factor 1: “Full-length ARF1-GDP-mg in complex with brefeldin a and a SEC7 domain”. X-ray diffraction, 4 ligands (G3D, AFB, MG), 6 pockets (best druggability 0.78). MolNFT v1 #20246 on GenesisL1: 3D structure…
- PDB
- 1R8Q
- Type
- protein
- Length
- 743 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor 1; Arno
- UniProt
- P84080, Q99418
- Ligands
- G3D, AFB, MG, ZN
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor 1 | protein | 179 | 36% helix, 20% strand | P84080 |
| E | Arno | protein | 191 | 64% helix, 2% strand | Q99418 |
| F | Arno | protein | 194 | 65% helix, 2% strand | Q99418 |
Ligands and binding sites
- G3D · Guanosine-3'-monophosphate-5'-diphosphate · ligand · 2 copies · chains A, B
- AFB · 1,6,7,8,9,11A,12,13,14,14A-decahydro-1,13-dihydroxy-6-methyl-4H-cyclopent[f]oxacyclotridecin-4-one · ligand · 2 copies · chains A, E, B, F
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.78 | 0.85 | 68 | MG, AFB |
| 2 | 873 | 0.77 | 0.80 | 95 | empty |
| 3 | 541 | 0.76 | 0.84 | 57 | MG, AFB |
| 4 | 423 | 0.67 | 0.80 | 55 | empty |
| 5 | 56 | 0.30 | 0.75 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1421 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1378 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 446 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 408 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 365 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1R8Q · Full-length ARF1-GDP-mg in complex with brefeldin a and a SEC7 domain · the same entry in another collection · chain F against F, TM-score 1.00
- Q99418 · AlphaFold monomer V2.0 prediction for cytohesin-2 (Q99418) · a predicted model of the same protein · chain E against A, TM-score 0.90
- P84080 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P84080) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P84080
- Every structure of UniProt Q99418
- Elsewhere: RCSB PDB 1R8Q · PDBe 1R8Q · UniProt P84080 · UniProt Q99418
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