Research workbench
Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (ZA3)
Analyse Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (ZA3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y2I
- Type
- protein
- Length
- 467 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
- ZA3, NA, CL, SO4
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 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 | 467 | 38% helix, 20% strand | Q7CRA4 |
Ligands and binding sites
- ZA3 · Trihydroxy-[[(2-nitrophenyl)carbonylamino]methyl]boron · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 11 copies · chains A
- SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.52 | 0.76 | 33 | ZA3, NA |
| 2 | 107 | 0.43 | 0.77 | 23 | SO4, CL |
| 3 | 102 | 0.36 | 0.74 | 22 | empty |
| 4 | 55 | 0.29 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Y2I · Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (ZA3) · 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 2Y2I · PDBe 2Y2I · UniProt Q7CRA4
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