Research workbench
Crystal structure of staphylococcus aureus metallopeptidase (SAPEP/DAPE) in the apo-form
Analyse Crystal structure of staphylococcus aureus metallopeptidase (SAPEP/DAPE) in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KHX
- Type
- protein
- Length
- 847 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dipeptidase SACOL1801
- EC
- 3.4.13.-
- UniProt
- Q5HF23
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dipeptidase SACOL1801 (EC 3.4.13.-) | protein | 422 | 33% helix, 26% strand | Q5HF23 |
| B | Putative dipeptidase SACOL1801 (EC 3.4.13.-) | protein | 425 | 34% helix, 27% strand | Q5HF23 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.54 | 0.77 | 38 | empty |
| 2 | 106 | 0.45 | 0.79 | 24 | empty |
| 3 | 79 | 0.38 | 0.78 | 27 | empty |
| 4 | 76 | 0.37 | 0.77 | 20 | empty |
| 5 | 92 | 0.35 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3KHX · Crystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the apo-form · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HF23 · AlphaFold monomer V2.0 prediction for putative dipeptidase SACOL1801 (Q5HF23) · a predicted model of the same protein · chain B against A, TM-score 0.51
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 Q5HF23
- Elsewhere: RCSB PDB 3KHX · PDBe 3KHX · UniProt Q5HF23
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