Research workbench
Crystal structure of the degs protease in complex with the ywf activating peptide
Analyse Crystal structure of the degs protease in complex with the ywf activating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R3Y
- Type
- protein
- Length
- 841 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease degs; Synthetic peptide ywf
- EC
- 3.4.21.-
- UniProt
- P0AEE3
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease degs (EC 3.4.21.-) | protein | 280 | 14% helix, 34% strand | P0AEE3 |
| B | Protease degs (EC 3.4.21.-) | protein | 274 | 14% helix, 34% strand | P0AEE3 |
| C | Protease degs (EC 3.4.21.-) | protein | 275 | 14% helix, 36% strand | P0AEE3 |
| D, E, F | Synthetic peptide ywf | protein | 4 | 0% helix, 25% strand | — |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.70 | 0.89 | 28 | empty |
| 2 | 56 | 0.70 | 0.98 | 19 | empty |
| 3 | 157 | 0.68 | 0.87 | 30 | empty |
| 4 | 131 | 0.66 | 0.88 | 31 | empty |
| 5 | 359 | 0.66 | 0.80 | 54 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1162 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1096 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1081 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 530 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 518 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2R3Y · Crystal structure of the DegS protease in complex with the YWF activating peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P0AEE3 · AlphaFold monomer V2.0 prediction for serine endoprotease degs (P0AEE3) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 2R3Y · PDBe 2R3Y · UniProt P0AEE3
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