Research workbench
Structure of penicillin-binding protein 5 from E. COLI: imipenem acyl- enzyme complex
Analyse Structure of penicillin-binding protein 5 from E. COLI: imipenem acyl- enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MZF
- Type
- protein
- Length
- 355 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase daca
- EC
- 3.4.16.4, 3.5.2.6
- UniProt
- P0AEB2
- Ligands
- IM2
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-D-alanine carboxypeptidase daca (EC 3.4.16.4, 3.5.2.6) | protein | 355 | 30% helix, 33% strand | P0AEB2 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic 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 | 163 | 0.47 | 0.76 | 27 | IM2 |
| 2 | 151 | 0.44 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3MZF · Structure of penicillin-binding protein 5 from E. coli: imipenem acyl-enzyme complex · 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 3MZF · PDBe 3MZF · UniProt P0AEB2
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