3ESW: Complex of yeast PNGase with GlcNAc2-IAc

Complex of yeast PNGase with GlcNAc2-IAc. Determined by X-ray diffraction at 3.4 Å resolution. Released 11 Nov 2008.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,220
Mol. weight: 48.24 kDa
Ligands: ZN
Released: 11 Nov 2008

Explore 3ESW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ESW contains 24 α-helices and 14 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1-2	2
α-helix	12-30	19
α-helix	36-48	13
α-helix	50-62	13
α-helix	69-78	10
α-helix	81-93	13
α-helix	103-114	12
α-helix	115-120	6
β-strand	122-123	2	1
α-helix	127-129	3
β-strand	140-146	7	2
α-helix	150-153	4
β-strand	157-165	9	2
β-strand	171-177	7	2
α-helix	180-186	7
β-strand	188-189	2	1
α-helix	191-204	14
β-strand	209-214	6	3
β-strand	218-225	8	3
α-helix	226-228	3
β-strand	230-234	5	3
β-strand	235	1	4
β-strand	240	1	4
α-helix	245-246	2
α-helix	247-251	5
β-strand	255	1	5
β-strand	258-262	5	3
β-strand	265-268	4	3
α-helix	270-273	4
β-strand	278	1	5
α-helix	279-280	2
α-helix	286-299	14
α-helix	306-324	19

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	259-268	10
α-helix	273-275	3
α-helix	276-286	11
α-helix	288-296	9
α-helix	298-305	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase	A	protein	355	Saccharomyces cerevisiae	Q02890 (AlphaFold model)
UV excision repair protein RAD23	B	protein	55	Saccharomyces cerevisiae	P32628 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3ESW_1 Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase (chains A)
MGSSHHHHHHSSGLVPRGSHMNNIDFDSIAKMLLIKYKDFILSKFKKAAPVENIRFQNLV
HTNQFAQGVLGQSQHLCTVYDNPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTD
YLVKELLRYFKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCN
RCGNITRFPRYNDPIKLLETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSN
FLNRWVHVDSCEQSFDQPYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQNELPRDQIKE
EDLKFLCQFITKRLRYSLNDDEIYQLACRDEQEQIELIRGKTQETKSESVSAASK

Sequence of entity 2 (B), FASTA

>3ESW_2 UV excision repair protein RAD23 (chains B)
SIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase. Zhao, G., Li, G., Zhou, X. et al. Glycobiology (2009) 19:118-125. DOI 10.1093/glycob/cwn108 · PubMed

Other PDB entries of the same protein (UniProt Q02890 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1X3Z 2.8 Å, Structure of a peptide:N-glycanase-Rad23 complex
1X3W 3.0 Å, Structure of a peptide:N-glycanase-Rad23 complex

Browse structure collections

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