MolNFT v1 · #190586 · protein
Cryo-EM structure of EDS1 and SAG101 with ATP-apdr
7XJP · Protein EDS1: “Cryo-EM structure of EDS1 and SAG101 with ATP-apdr”. Electron microscopy, 2 ligands (APR, ATP), 20 pockets (best druggability 0.82). MolNFT v1 #190586 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XJP
- Type
- protein
- Length
- 1,089 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein EDS1; Senescence-associated carboxylesterase 101
- EC
- 3.1.1.1
- UniProt
- Q9SU72, Q4F883
- Ligands
- APR, ATP
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein EDS1 | protein | 580 | 57% helix, 9% strand | Q9SU72 |
| B | Senescence-associated carboxylesterase 101 (EC 3.1.1.1) | protein | 509 | 55% helix, 9% strand | Q4F883 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.82 | 0.84 | 87 | APR, ATP |
| 2 | 891 | 0.76 | 0.79 | 80 | empty |
| 3 | 316 | 0.68 | 0.83 | 35 | empty |
| 4 | 539 | 0.66 | 0.77 | 52 | empty |
| 5 | 310 | 0.61 | 0.78 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2539 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7XJP · Cryo-EM structure of EDS1 and SAG101 with ATP-APDR · 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
- Q4F883 · AlphaFold monomer V2.0 prediction for senescence-associated carboxylesterase 101 (Q4F883) · a predicted model of the same protein · chain B against A, TM-score 0.73
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 Q4F883
- Elsewhere: RCSB PDB 7XJP · PDBe 7XJP · UniProt Q9SU72 · UniProt Q4F883
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