Research workbench
Crystal structure of degs H198P/D320A mutant modified by dfp and in complex with yrf peptide
Analyse Crystal structure of degs H198P/D320A mutant modified by dfp and in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GDU
- Type
- protein
- Length
- 876 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Degs protease; Yrf peptide
- EC
- 3.4.21.-
- UniProt
- P0AEE3
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Degs protease (EC 3.4.21.-) | protein | 295 | 16% helix, 38% strand | P0AEE3 |
| B | Degs protease (EC 3.4.21.-) | protein | 279 | 15% helix, 32% strand | P0AEE3 |
| C | Degs protease (EC 3.4.21.-) | protein | 293 | 15% helix, 42% strand | P0AEE3 |
| D, E, F | Yrf peptide | protein | 3 | 0% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.64 | 0.81 | 34 | empty |
| 2 | 313 | 0.62 | 0.79 | 38 | empty |
| 3 | 273 | 0.60 | 0.79 | 55 | empty |
| 4 | 236 | 0.58 | 0.79 | 29 | empty |
| 5 | 104 | 0.51 | 0.82 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1276 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1272 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1153 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 501 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 453 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 3GDU · Crystal structure of DegS H198P/D320A mutant modified by DFP and in complex with YRF… · 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 0.96
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 3GDU · PDBe 3GDU · UniProt P0AEE3
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