Research workbench
Crystal structure of penicillin binding protein 4 from staphylococcus aureus col in complex with ampicillin
Analyse Crystal structure of penicillin binding protein 4 from staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HUN
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 4
- EC
- 3.4.16.4
- UniProt
- Q5HI26
- Ligands
- ZZ7
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Penicillin-binding protein 4 (EC 3.4.16.4) | protein | 359 | 33% helix, 26% strand | Q5HI26 |
Ligands and binding sites
- ZZ7 · (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.74 | 0.80 | 65 | empty |
| 2 | 126 | 0.49 | 0.80 | 26 | ZZ7 |
| 3 | 125 | 0.46 | 0.78 | 27 | ZZ7 |
| 4 | 98 | 0.34 | 0.73 | 23 | empty |
| 5 | 55 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3HUN · Crystal structure of Penicillin binding protein 4 from Staphylococcus aureus COL 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 Q5HI26
- Elsewhere: RCSB PDB 3HUN · PDBe 3HUN · UniProt Q5HI26
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