Research workbench
Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (ZA4)
Analyse Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (ZA4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y2J
- Type
- protein
- Length
- 470 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- EC
- 2.4.1.129, 2.3.2.-
- UniProt
- Q7CRA4
- Ligands
- ZA4, NA, CL, SO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 37% 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 | 470 | 37% helix, 20% strand | Q7CRA4 |
Ligands and binding sites
- ZA4 · [(2-fluorophenyl)carbonylamino]methyl-trihydroxy-boron · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 15 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.49 | 0.75 | 32 | ZA4, NA |
| 2 | 103 | 0.42 | 0.77 | 24 | CL |
| 3 | 98 | 0.35 | 0.74 | 21 | empty |
| 4 | 54 | 0.29 | 0.75 | 18 | EDO |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Y2J · Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (ZA4) · 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 2Y2J · PDBe 2Y2J · UniProt Q7CRA4
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