MolNFT v1 · #49953 · protein
Crystal structure of the degs protease in complex with the ywf activating peptide
2R3Y · Protease degs: “Crystal structure of the degs protease in complex with the ywf activating peptide”. X-ray diffraction, 12 pockets (best druggability 0.70). MolNFT v1 #49953 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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