Research workbench
Crystal structure of staphylococcus aureus metallopeptidase (SAPEP/DAPE) in the MN2+ bound 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
- 3KI9
- Type
- protein
- Length
- 467 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dipeptidase SACOL1801
- EC
- 3.4.13.-
- UniProt
- Q5HF23
- Ligands
- MN, PO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dipeptidase SACOL1801 (EC 3.4.13.-) | protein | 467 | 33% helix, 27% strand | Q5HF23 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.66 | 0.82 | 47 | PO4 |
| 2 | 88 | 0.47 | 0.81 | 21 | empty |
| 3 | 51 | 0.42 | 0.83 | 16 | empty |
Compared structures
- 3KI9 · Crystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the Mn2+… · 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 A against A, TM-score 0.86
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 3KI9 · PDBe 3KI9 · UniProt Q5HF23
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