Research workbench
Crystal structure of penicillin-binding protein 4 (PBP4) from enterococcus faecalis in the ceftaroline-bound form
Analyse Crystal structure of penicillin-binding protein 4 (PBP4) from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MKI
- Type
- protein
- Length
- 419 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 4 (PBP4)
- UniProt
- Q9K3C9
- Ligands
- AI8, PO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 4 (PBP4) | protein | 419 | 35% helix, 20% strand | Q9K3C9 |
Ligands and binding sites
- AI8 · Ceftaroline, bound form · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.42 | 0.74 | 25 | AI8, PO4 |
| 2 | 63 | 0.34 | 0.77 | 18 | empty |
| 3 | 83 | 0.33 | 0.74 | 20 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MKI · Crystal structure of penicillin-binding protein 4 (PBP4) from Enterococcus faecalis in… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9K3C9
- Elsewhere: RCSB PDB 6MKI · PDBe 6MKI · UniProt Q9K3C9
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