Research workbench
EDS1-PAD4 complexed with prib-ADP
Analyse EDS1-PAD4 complexed with prib-ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XEY
- Type
- protein
- Length
- 1,133 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein EDS1; Lipase-like PAD4
- EC
- 2.3.1.-
- UniProt
- Q9SU72, Q9S745
- Ligands
- ADP, RP5
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein EDS1 | protein | 614 | 62% helix, 9% strand | Q9SU72 |
| B | Lipase-like PAD4 (EC 2.3.1.-) | protein | 519 | 56% helix, 10% strand | Q9S745 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.83 | 0.85 | 92 | empty |
| 2 | 554 | 0.83 | 0.88 | 46 | ADP, RP5 |
| 3 | 96 | 0.77 | 0.98 | 26 | empty |
| 4 | 481 | 0.74 | 0.83 | 53 | empty |
| 5 | 275 | 0.61 | 0.79 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 3232 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 7XEY · EDS1-PAD4 complexed with pRib-ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SU72 · AlphaFold monomer V2.0 prediction for protein EDS1 (Q9SU72) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9S745 · AlphaFold monomer V2.0 prediction for lipase-like PAD4 (Q9S745) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q9SU72
- Every structure of UniProt Q9S745
- Elsewhere: RCSB PDB 7XEY · PDBe 7XEY · UniProt Q9SU72 · UniProt Q9S745
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.