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Oxa-10 beta-lactamase with covalent modification

Analyse Oxa-10 beta-lactamase with covalent modification in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7B3U
Type
protein
Length
493 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Beta-lactamase oxa-10
EC
3.5.2.6
UniProt
P14489
Ligands
NA, SO4
Pockets
4 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABeta-lactamase oxa-10 (EC 3.5.2.6)protein24640% helix, 24% strandP14489
BBeta-lactamase oxa-10 (EC 3.5.2.6)protein24738% helix, 23% strandP14489

Ligands and binding sites

  • NA · Sodium ion · metal · 2 copies · chains A
  • SO4 · Sulfate ion · ion · 6 copies · chains A, B
  • PEG · Di(hydroxyethyl)ether · additive · chains A

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11420.750.9336empty
21400.720.9131empty
31280.400.7527SO4
41150.380.7425SO4

Interfaces

1 interface between chains.

  • A–B · 1187 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

  • 7B3U · OXA-10 beta-lactamase with covalent modification · the same entry in another collection · chain A against A, TM-score 1.00
  • P14489 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-10 (P14489) · a predicted model of the same protein · chain A against A, TM-score 0.99

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