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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
- 2JE5
- Type
- protein
- Length
- 923 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- UniProt
- O70038
- Ligands
- L4C, CL, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B | protein | 461 | 38% helix, 19% strand | O70038 |
| B | Penicillin-binding protein 1B | protein | 462 | 37% helix, 19% strand | O70038 |
Ligands and binding sites
- L4C · (2E)-2-{[(2S)-2-(acetylamino)-2-carboxyethoxy]imino}pentanedioic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.71 | 0.77 | 81 | L4C |
| 2 | 155 | 0.42 | 0.75 | 21 | CL |
| 3 | 118 | 0.41 | 0.76 | 21 | CL |
| 4 | 104 | 0.40 | 0.76 | 17 | CL |
| 5 | 103 | 0.38 | 0.75 | 22 | SO4 |
Interfaces
1 interface between chains.
- A–B · 581 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2JE5 · 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 2JE5 · PDBe 2JE5 · UniProt O70038
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