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Crystal structure of the zinc-beta-lactamase L1 from stenotrophomonas maltophilia (inhibitor 2)
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
- 2GFK
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- 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
- VII, ZN, SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 266 | 31% helix, 24% strand | P52700 |
Ligands and binding sites
- VII · 2,5-diphenylfuran-3,4-dicarboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.63 | 0.81 | 38 | empty |
| 2 | 172 | 0.48 | 0.76 | 29 | ZN, VII |
| 3 | 157 | 0.47 | 0.76 | 30 | VII |
| 4 | 65 | 0.29 | 0.74 | 16 | empty |
| 5 | 51 | 0.26 | 0.74 | 12 | PEG |
Interfaces
1 interface between chains.
- A–B · 1311 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2GFK · 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 B 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 2GFK · PDBe 2GFK · UniProt P52700
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