Research workbench
Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (MP2 inhibitor complex)
Analyse Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (MP2 inhibitor complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FU9
- 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
- MP2, ZN, SO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 266 | 32% helix, 24% strand | P52700 |
Ligands and binding sites
- MP2 · N-[(benzyloxy)carbonyl]-L-cysteinylglycine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.64 | 0.82 | 37 | empty |
| 2 | 120 | 0.42 | 0.76 | 30 | MP2 |
| 3 | 113 | 0.39 | 0.75 | 27 | ZN, MP2 |
| 4 | 53 | 0.29 | 0.75 | 19 | empty |
| 5 | 60 | 0.28 | 0.74 | 12 | GOL |
Interfaces
1 interface between chains.
- A–B · 1371 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2FU9 · Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (mp2 inhibitor complex) · 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 2FU9 · PDBe 2FU9 · UniProt P52700
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