1X3Z: Peptide:N-glycanase-Rad23 complex

Structure of a peptide:N-glycanase-Rad23 complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 14 Jun 2005.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 3,197
Mol. weight: 48.09 kDa
Ligands: ZN
Released: 14 Jun 2005

Explore 1X3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1X3Z contains 20 α-helices and 13 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	36-48	13
α-helix	50-65	16
α-helix	69-78	10
α-helix	81-94	14
α-helix	103-114	12
α-helix	115-120	6
β-strand	122-123	2	1
β-strand	140-146	7	2
α-helix	151-153	3
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	191-203	13
β-strand	209-214	6	3
β-strand	218-225	8	3
β-strand	230-235	6	3
β-strand	240-241	2	3
α-helix	245	1
α-helix	246-250	5
β-strand	255	1	4
β-strand	258-262	5	3
β-strand	265-268	4	3
α-helix	270-273	4
β-strand	278	1	4
α-helix	286-301	16
α-helix	306-324	19

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	261-271	11
α-helix	273-275	3
α-helix	276-284	9
α-helix	288-295	8
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)
peptide PHQ-Val-Ala-Asp-CF0	I	protein	5

Sequence of entity 1 (A), FASTA

>1X3Z_1 peptide: N-glycanase (chains A)
NNIDFDSIAKMLLIKYKDFILSKFKKAAPVENIRFQNLVHTNQFAQGVLGQSQHLCTVYD
NPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTDYLVKELLRYFKQDFFKWCNKP
DCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPRYNDPIKLLETR
KGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFDQPYIY
SINWNKKMSYCIAFGKDGVVDVSKRYILQNELPRDQIKEEDLKFLCQFITKRLRYSLNDD
EIYQLACRDEQEQIELIRGKTQETKSESVSAASKS

Sequence of entity 2 (B), FASTA

>1X3Z_2 UV excision repair protein RAD23 (chains B)
GTTGGATDAAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMAN
PEVFVSMLLEAV

Sequence of entity 3 (I), FASTA

>1X3Z_3 peptide PHQ-Val-Ala-Asp-CF0 (chains I)
XVADX

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:

1X3W 3.0 Å, Structure of a peptide:N-glycanase-Rad23 complex
3ESW 3.4 Å, Complex of yeast PNGase with GlcNAc2-IAc.

Browse structure collections

About this viewer

MolViewer shows 1X3Z directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.