Research workbench
Structural and mechanistic basis of penicillin binding protein inhibition by lactivicins
Analyse Structural and mechanistic basis of penicillin binding protein inhibition by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JCH
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- UniProt
- O70038
- Ligands
- PL7, SO4, CL
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B | protein | 461 | 35% helix, 20% strand | O70038 |
Ligands and binding sites
- PL7 · (2E)-2-({(2S)-2-carboxy-2-[(phenoxyacetyl)amino]ethoxy}imino)pentanedioic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.58 | 0.78 | 31 | PL7 |
| 2 | 223 | 0.48 | 0.74 | 33 | SO4 |
| 3 | 73 | 0.33 | 0.75 | 20 | empty |
| 4 | 52 | 0.27 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2JCH · Structural and mechanistic basis of penicillin binding protein inhibition by lactivicins · 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 O70038
- Elsewhere: RCSB PDB 2JCH · PDBe 2JCH · UniProt O70038
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.