MolNFT v1 · #180624 · protein
Crystal structure of the oxacillin-hydrolyzing class D extended- spectrum beta-lactamase oxa-14 from pseudomonas aeruginosa in complex with covalently bound clavulanic acid
7L5T: “Crystal structure of the oxacillin-hydrolyzing class D extended- spectrum beta-lactamase oxa-14 from…”. X-ray diffraction, 3 ligands (ISS, SO4, CL), 4 pockets (best druggability 0.72). MolNFT v1 #180624 on GenesisL1: 3D structure…
- PDB
- 7L5T
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q59648
- Ligands
- ISS, SO4, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 246 | 40% helix, 23% strand | Q59648 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 247 | 36% helix, 24% strand | Q59648 |
Ligands and binding sites
- ISS · (2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 15 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.72 | 0.91 | 31 | empty |
| 2 | 374 | 0.68 | 0.81 | 59 | ISS, SO4, CL |
| 3 | 141 | 0.42 | 0.75 | 27 | ISS, SO4, CL |
| 4 | 57 | 0.39 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1278 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 7L5T · Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase… · 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 Q59648
- Elsewhere: RCSB PDB 7L5T · PDBe 7L5T · UniProt Q59648
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