Research workbench
Crystal structure of salmonella effector in complex with NAD and host co-factor ARF1
Analyse Crystal structure of salmonella effector in complex with NAD and host co-factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DN9
- Type
- protein
- Length
- 1,840 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cytoplasmic protein; ADP-ribosylation factor 1
- UniProt
- Q8ZPY9, P84077
- Ligands
- NAD, GDP, MG
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Putative cytoplasmic protein | protein | 299 | 42% helix, 14% strand | Q8ZPY9 |
| B, D, F, H | ADP-ribosylation factor 1 | protein | 161 | 35% helix, 27% strand | P84077 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, E, C, G
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains B, D, F, H
- MG · Magnesium ion · metal · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.73 | 0.79 | 65 | NAD |
| 2 | 717 | 0.72 | 0.78 | 58 | NAD |
| 3 | 755 | 0.72 | 0.78 | 63 | NAD |
| 4 | 299 | 0.61 | 0.79 | 31 | NAD |
| 5 | 338 | 0.61 | 0.78 | 44 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1470 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1460 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1452 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1442 Ų buried · 12 hydrogen bonds · protein-protein
- E–G · 911 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7DN9 · Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1 · the same entry in another collection · chain H against H, TM-score 1.00
- P84077 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P84077) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 Q8ZPY9
- Every structure of UniProt P84077
- Elsewhere: RCSB PDB 7DN9 · PDBe 7DN9 · UniProt Q8ZPY9 · UniProt P84077
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