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Oxa-48 bound by compound 2.2

Analyse Oxa-48 bound by compound 2.2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XQR
Type: protein
Length: 484 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q6XEC0
Ligands: VBV, CL
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase (EC 3.5.2.6)	protein	242	41% helix, 21% strand	Q6XEC0

Ligands and binding sites

VBV · [1,1'-biphenyl]-4,4'-disulfonic acid · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	870	0.77	0.80	119	VBV, CL
2	50	0.35	0.79	14	empty

Interfaces

1 interface between chains.

A–B · 1010 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

6XQR · OXA-48 bound by Compound 2.2 · 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 Q6XEC0
Elsewhere: RCSB PDB 6XQR · PDBe 6XQR · UniProt Q6XEC0

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