Research workbench
Crystal structure of the zinc-beta-lactamase L1 from stenotrophomonas maltophilia (inhibitor 3)
Analyse Crystal structure of the zinc-beta-lactamase L1 from stenotrophomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HB9
- Type
- protein
- Length
- 266 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase L1
- EC
- 3.5.2.6
- UniProt
- P52700
- Ligands
- L13, ZN, SO4
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 266 | 30% helix, 23% strand | P52700 |
Ligands and binding sites
- L13 · 4-amino-5-(2-methylphenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.47 | 0.77 | 29 | L13 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2HB9 · Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophomonas Maltophilia… · the same entry in another collection · chain A against A, TM-score 1.00
- P52700 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase L1 type 3 (P52700) · 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 P52700
- Elsewhere: RCSB PDB 2HB9 · PDBe 2HB9 · UniProt P52700
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