Research workbench
E. COLI PBP1B in complex with acyl-ampicillin and moenomycin
Analyse E. COLI PBP1B in complex with acyl-ampicillin and moenomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HL9
- Type
- protein
- Length
- 695 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
- AIX, M0E
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 3.4.-.-) | protein | 695 | 39% helix, 20% strand | P02919 |
Ligands and binding sites
- AIX · (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · chains A
- M0E · Moenomycin · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.71 | 0.82 | 37 | empty |
| 2 | 319 | 0.67 | 0.82 | 38 | empty |
| 3 | 464 | 0.65 | 0.78 | 44 | empty |
| 4 | 106 | 0.53 | 0.83 | 22 | empty |
| 5 | 261 | 0.52 | 0.75 | 37 | AIX |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5HL9 · E. coli PBP1b in complex with acyl-ampicillin 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 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 P02919
- Elsewhere: RCSB PDB 5HL9 · PDBe 5HL9 · UniProt P02919
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