Research workbench
Crystal structure of degs stress sensor protease in complex with activating dnrlglvyqf peptide
Analyse Crystal structure of degs stress sensor protease in complex with activating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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