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Crystal structure of penicillin binding protein 4 (dacb) from escherichia COLI, complexed with penicillin-V
Analyse Crystal structure of penicillin binding protein 4 (dacb) from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EX9
- Type
- protein
- Length
- 442 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 4
- EC
- 3.4.16.4, 3.4.99.-
- UniProt
- P24228
- Ligands
- 35P
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 4 (EC 3.4.16.4, 3.4.99.-) | protein | 442 | 32% helix, 28% strand | P24228 |
Ligands and binding sites
- 35P · (2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.33 | 0.74 | 21 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2EX9 · Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P24228 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase dacb (P24228) · a predicted model of the same protein · 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 P24228
- Elsewhere: RCSB PDB 2EX9 · PDBe 2EX9 · UniProt P24228
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