Research workbench
E. COLI PBP1B in complex with acyl-aztreonam and moenomycin
Analyse E. COLI PBP1B in complex with acyl-aztreonam and moenomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HLB
- Type
- protein
- Length
- 733 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, 3.4.-.-
- UniProt
- P02919
- Ligands
- M0E, AZR
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 3.4.-.-) | protein | 733 | 40% helix, 19% strand | P02919 |
Ligands and binding sites
- M0E · Moenomycin · ligand · chains A
- AZR · 2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S, 3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.78 | 0.81 | 78 | empty |
| 2 | 413 | 0.69 | 0.81 | 46 | empty |
| 3 | 83 | 0.52 | 0.84 | 18 | empty |
| 4 | 230 | 0.50 | 0.76 | 39 | AZR |
| 5 | 182 | 0.49 | 0.76 | 21 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5HLB · E. coli PBP1b in complex with acyl-aztreonam and moenomycin · the same entry in another collection · chain A against A, TM-score 1.00
- P02919 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 1B (P02919) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P02919
- Elsewhere: RCSB PDB 5HLB · PDBe 5HLB · UniProt P02919
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