Research workbench
Crystal structure of E. COLI penicillin-binding protein 5 in complex with a peptide-mimetic penicillin
Analyse Crystal structure of E. COLI penicillin-binding protein 5 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BEB
- Type
- protein
- Length
- 354 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 5
- EC
- 3.4.16.4, 3.5.2.6
- UniProt
- P0AEB2
- Ligands
- HJ3
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 5 (EC 3.4.16.4, 3.5.2.6) | protein | 354 | 28% helix, 32% strand | P0AEB2 |
Ligands and binding sites
- HJ3 · (2R,4S)-2-[(1R)-1-{[(6S)-6-amino-6-carboxyhexanoyl]amino}-2-oxoethyl]-5,5-dimethyl-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
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.45 | 0.75 | 25 | empty |
| 2 | 153 | 0.45 | 0.76 | 28 | HJ3 |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3BEB · Crystal structure of E. coli penicillin-binding protein 5 in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AEB2 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase daca (P0AEB2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0AEB2
- Elsewhere: RCSB PDB 3BEB · PDBe 3BEB · UniProt P0AEB2
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