Research workbench
Penicillin-binding protein 1b (pbp-1b) in complex with an alkyl boronate (z10)
Analyse Penicillin-binding protein 1b (pbp-1b) in complex with an alkyl boronate (z10) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y2P
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.62
- Source
- STREPTOCOCCUS PNEUMONIAE
- Molecule
- Penicillin-binding protein 1B
- EC
- 2.4.1.129, 2.3.2.-
- UniProt
- Q7CRA4
- Ligands
- Z10, NA, CL
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · resolution 1.62 · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 2.3.2.-) | protein | 466 | 38% helix, 20% strand | Q7CRA4 |
Ligands and binding sites
- Z10 · [(1S)-1-[(2-fluoro-6-phenyl-phenyl)carbonylamino]ethyl]-trihydroxy-boron · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 20 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.54 | 0.76 | 32 | Z10, NA |
| 2 | 157 | 0.43 | 0.74 | 27 | CL |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Y2P · Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (Z10) · 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 Q7CRA4
- Elsewhere: RCSB PDB 2Y2P · PDBe 2Y2P · UniProt Q7CRA4
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