MolNFT v1 · #148077 · protein
Crystal structure of degs stress sensor protease in complex with activating dnrlglvyqf peptide
6EW9 · Serine endoprotease degs: “Crystal structure of degs stress sensor protease in complex with activating dnrlglvyqf peptide”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.60). MolNFT v1 #148077 on GenesisL1: 3D…
- PDB
- 6EW9
- Type
- protein
- Length
- 914 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine endoprotease degs; Dnrlglvyqf peptide
- EC
- 3.4.21.107
- UniProt
- P0AEE3
- Ligands
- CA
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine endoprotease degs (EC 3.4.21.107) | protein | 305 | 15% helix, 39% strand | P0AEE3 |
| B | Serine endoprotease degs (EC 3.4.21.107) | protein | 292 | 16% helix, 37% strand | P0AEE3 |
| C | Serine endoprotease degs (EC 3.4.21.107) | protein | 302 | 15% helix, 39% strand | P0AEE3 |
| P, Q, R | Dnrlglvyqf peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.60 | 0.79 | 52 | CA |
| 2 | 112 | 0.51 | 0.81 | 23 | empty |
| 3 | 115 | 0.46 | 0.79 | 25 | empty |
| 4 | 91 | 0.44 | 0.79 | 20 | empty |
| 5 | 74 | 0.41 | 0.80 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1177 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1130 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1074 Ų buried · 26 hydrogen bonds · protein-protein
- C–R · 615 Ų buried · 11 hydrogen bonds · protein-protein
- A–P · 562 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6EW9 · Crystal structure of degs stress sensor protease in complex with activating dnrlglvyqf… · the same entry in another collection · chain R against R, TM-score 1.00
- P0AEE3 · AlphaFold monomer V2.0 prediction for serine endoprotease degs (P0AEE3) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P0AEE3
- Elsewhere: RCSB PDB 6EW9 · PDBe 6EW9 · UniProt P0AEE3
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