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Crystal structure of degs H198P/D320A mutant modified by dfp in complex with dnrdgnvyqf omp peptide
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
- 3GCO
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease degs; Dnrdgnvyqf peptide
- EC
- 3.4.21.-
- UniProt
- P0AEE3
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease degs (EC 3.4.21.-) | protein | 303 | 15% helix, 36% strand | P0AEE3 |
| B | Dnrdgnvyqf peptide | protein | 4 | 0% helix, 50% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.74 | 0.93 | 30 | empty |
| 2 | 288 | 0.60 | 0.79 | 34 | empty |
| 3 | 77 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3GCO · Crystal structure of DegS H198P/D320A mutant modified by DFP in complex with DNRDGNVYQF… · 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 3GCO · PDBe 3GCO · UniProt P0AEE3
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