Research workbench
Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (cu- substituted form)
Analyse Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (cu- substituted form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FU7
- 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
- PHN, CU, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 266 | 31% helix, 23% strand | P52700 |
Ligands and binding sites
- PHN · 1,10-phenanthroline · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
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 | 514 | 0.79 | 0.86 | 36 | empty |
| 2 | 53 | 0.67 | 0.96 | 22 | empty |
| 3 | 126 | 0.42 | 0.76 | 27 | CU |
| 4 | 102 | 0.38 | 0.75 | 15 | empty |
| 5 | 116 | 0.37 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 764 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2FU7 · Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (Cu-substituted form) · 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 2FU7 · PDBe 2FU7 · UniProt P52700
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