MolNFT v1 · #190524 · protein
Cryo-EM structure of EDS1 and PAD4
7XDD · Lipase-like PAD4: “Cryo-EM structure of EDS1 and PAD4”. Electron microscopy, 11 pockets (best druggability 0.75). MolNFT v1 #190524 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XDD
- Type
- protein
- Length
- 1,123 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase-like PAD4; Protein EDS1
- EC
- 2.3.1.-
- UniProt
- Q9S745, Q9SU72
- Pockets
- 11 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase-like PAD4 (EC 2.3.1.-) | protein | 512 | 54% helix, 10% strand | Q9S745 |
| B | Protein EDS1 | protein | 611 | 60% helix, 9% strand | Q9SU72 |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.75 | 0.97 | 28 | empty |
| 2 | 926 | 0.73 | 0.77 | 67 | empty |
| 3 | 683 | 0.73 | 0.79 | 68 | empty |
| 4 | 583 | 0.70 | 0.79 | 63 | empty |
| 5 | 350 | 0.66 | 0.80 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 2260 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7XDD · Cryo-EM structure of EDS1 and PAD4 · 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 B 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 A against A, TM-score 0.77
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 Q9S745
- Every structure of UniProt Q9SU72
- Elsewhere: RCSB PDB 7XDD · PDBe 7XDD · UniProt Q9S745 · UniProt Q9SU72
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