Research workbench
Crystal structure of penicillin-binding protein 4 from listeria monocytogenes in the apo form
Analyse Crystal structure of penicillin-binding protein 4 from listeria monocytogenes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZG7
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 4
- UniProt
- Q8Y547
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 4 | protein | 40 | 28% helix, 23% strand | Q8Y547 |
| B | Penicillin-binding protein 4 | protein | 457 | 42% helix, 17% strand | Q8Y547 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.51 | 0.82 | 26 | empty |
| 2 | 209 | 0.48 | 0.75 | 33 | TLA |
| 3 | 143 | 0.42 | 0.75 | 25 | empty |
| 4 | 83 | 0.35 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1775 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3ZG7 · Crystal Structure of Penicillin-Binding Protein 4 from Listeria monocytogenes in the apo… · 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 Q8Y547
- Elsewhere: RCSB PDB 3ZG7 · PDBe 3ZG7 · UniProt Q8Y547
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