Research workbench
Crystal structure of degs H198P/D320A mutant modified by dfp in complex with omp peptide (yqf)
Analyse Crystal structure of degs H198P/D320A mutant modified by dfp in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GCN
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease degs; Yqf peptide
- EC
- 3.4.21.-
- UniProt
- P0AEE3
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease degs (EC 3.4.21.-) | protein | 301 | 15% helix, 38% strand | P0AEE3 |
| B | Yqf peptide | protein | 3 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.73 | 0.88 | 41 | empty |
| 2 | 243 | 0.59 | 0.79 | 28 | empty |
| 3 | 98 | 0.38 | 0.75 | 18 | empty |
| 4 | 63 | 0.36 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 454 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3GCN · Crystal structure of DegS H198P/D320A mutant modified by DFP in complex with OMP peptide… · the same entry in another collection · chain A against A, 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 0.97
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 3GCN · PDBe 3GCN · UniProt P0AEE3
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