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Crystal structure of the beta lactamase class D ybxi from nostoc

Analyse Crystal structure of the beta lactamase class D ybxi from nostoc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NHS
Type: protein
Length: 239 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
UniProt: Q8YU74
Ligands: CL
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase	protein	239	43% helix, 23% strand	Q8YU74

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A
FMT · Formic acid · additive · 5 copies · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	144	0.39	0.73	25	EDO, CL
2	70	0.31	0.75	18	empty

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

6NHS · Crystal Structure of the Beta Lactamase Class D YbXI from Nostoc · 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 Q8YU74
Elsewhere: RCSB PDB 6NHS · PDBe 6NHS · UniProt Q8YU74

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