1X3W: Peptide:N-glycanase-Rad23 complex

Structure of a peptide:N-glycanase-Rad23 complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 14 Jun 2005.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,187
Mol. weight: 48.2 kDa
Ligands: ZN
Released: 14 Jun 2005

Explore 1X3W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1X3W contains 20 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	12-30	19
α-helix	36-48	13
α-helix	50-62	13
α-helix	69-78	10
α-helix	81-94	14
α-helix	103-115	13
α-helix	116-120	5
β-strand	122-123	2	1
α-helix	127-129	3
β-strand	140-146	7	2
β-strand	157-165	9	2
β-strand	171-177	7	2
α-helix	182-184	3
β-strand	188-189	2	1
α-helix	191-203	13
β-strand	208-214	7	3
β-strand	218-225	8	3
β-strand	230-234	5	3
β-strand	235	1	4
β-strand	240	1	4
α-helix	246	1
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	286-301	16
α-helix	308-323	16

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	259-271	13
α-helix	273-275	3
α-helix	276-285	10
α-helix	288-296	9
α-helix	298-307	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
peptide:N-glycanase	A	protein	335	Saccharomyces cerevisiae	Q02890 (AlphaFold model)
UV excision repair protein RAD23	B	protein	72	Saccharomyces cerevisiae	P32628 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1X3W_1 peptide:N-glycanase (chains A)
NNIDFDSIAKMLLIKYKDFILSKFKKAAPVENIRFQNLVHTNQFAQGVLGQSQHLCTVYD
NPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTDYLVKELLRYFKQDFFKWCNKP
DCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPRYNDPIKLLETR
KGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFDQPYIY
SINWNKKMSYCIAFGKDGVVDVSKRYILQNELPRDQIKEEDLKFLCQFITKRLRYSLNDD
EIYQLACRDEQEQIELIRGKTQETKSESVSAASKS

Sequence of entity 2 (B), FASTA

>1X3W_2 UV excision repair protein RAD23 (chains B)
GTTGGATDAAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMAN
PEVFVSMLLEAV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins. Lee, J.H., Choi, J.M., Lee, C. et al. Proc Natl Acad Sci U S A (2005) 102:9144-9149. DOI 10.1073/pnas.0502082102 · 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
3ESW 3.4 Å, Complex of yeast PNGase with GlcNAc2-IAc.

Browse structure collections

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