Research workbench
Structural basis for the interaction of lactivicins with serine beta-lactamases
Analyse Structural basis for the interaction of lactivicins with serine beta-lactamases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X71
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P94458
- Ligands
- L4C, SO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 255 | 42% helix, 18% strand | P94458 |
Ligands and binding sites
- L4C · (2E)-2-{[(2S)-2-(acetylamino)-2-carboxyethoxy]imino}pentanedioic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains B
- EOH · Ethanol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.59 | 0.84 | 36 | empty |
| 2 | 160 | 0.54 | 0.80 | 34 | empty |
| 3 | 66 | 0.42 | 0.81 | 16 | empty |
| 4 | 55 | 0.41 | 0.81 | 16 | empty |
| 5 | 59 | 0.32 | 0.77 | 16 | L4C |
Interfaces
1 interface between chains.
- A–B · 678 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2X71 · Structural basis for the interaction of lactivicins with serine beta- lactamases · 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 P94458
- Elsewhere: RCSB PDB 2X71 · PDBe 2X71 · UniProt P94458
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