SAXSdb — 1x3w

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1. Protein Identity and Related Structures Protein Identity & Related Structures

peptide:N-glycanase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 8–342	Fragment：residues 8-342 Non-standard monomer：Yes (specific site not provided by mmCIF)	UV excision repair protein RAD23 × 1 （P32628） beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；291 K；sodium chloride, MES, pH 6, VAPOR DIFFUSION, temperature 291K	Resolution 3.00 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1X3W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ESW Complex of yeast PNGase with GlcNAc2-IAc. Deposited 2008-10-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 8–341（334 aa） Fragment：peptide:N-glycanase	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；291 K；0.1 M Tris-HCl, pH 8.5 and 2.0 M sodium chloride, EVAPORATION, temperature 291K	Resolution 3.40 Å R-free 0.235

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q02890_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–335； UniProt 8–342

UV excision repair protein RAD23

Saccharomyces cerevisiae

UniProt P32628

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 238–309	Fragment：XPC binding domain Non-standard monomer：Yes (specific site not provided by mmCIF)	peptide:N-glycanase × 1 （Q02890） beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；291 K；sodium chloride, MES, pH 6, VAPOR DIFFUSION, temperature 291K	Resolution 3.00 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1X3W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1X3Z Structure of a peptide:N-glycanase-Rad23 complex Deposited 2005-05-11	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 238–309（72 aa） Fragment：XPC binding domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；sodium chloride, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.270
2NBU Solution structure of the Rad23 ubiquitin-like (UBL) domain Deposited 2016-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–78（78 aa） Fragment：residues 1-78	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N] shuttling protein, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N] shuttling protein, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided
2NBW Solution structure of the Rpn1 T1 site with the Rad23 UBL domain Deposited 2016-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–78（78 aa） Fragment：residues 1-78	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.04-0.6 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.6 mM protein_1, 0.6 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided
2QSF Crystal structure of the Rad4-Rad23 complex Deposited 2007-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM sodium phosphate, 8% (w/v) PEG 2000, 2 mM dithiothreitol, pH 6.5, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.35 Å R-free 0.245
2QSG Crystal structure of Rad4-Rad23 bound to a UV-damaged DNA Deposited 2007-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100mM sodium chloride, 6% (v/v) isopropanol, 14 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP	Resolution 3.10 Å R-free 0.277
2QSH Crystal structure of Rad4-Rad23 bound to a mismatch DNA Deposited 2007-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100 mM sodium chloride, 15% (v/v) isopropanol, 10 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.81 Å R-free 0.244
3ESW Complex of yeast PNGase with GlcNAc2-IAc. Deposited 2008-10-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 254–308（55 aa） Fragment：XPCB Domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；291 K；0.1 M Tris-HCl, pH 8.5 and 2.0 M sodium chloride, EVAPORATION, temperature 291K	Resolution 3.40 Å R-free 0.235
3M62 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23 Deposited 2010-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–84（84 aa） Fragment：UNP residues 1-84, Ubiquitin-like domain	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.257
4YIR Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA Deposited 2015-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50mM BTP-HCl, 100mM NaCl, 14% isopropanol and 100mM calcium chloride	Resolution 3.05 Å R-free 0.253
6CFI Crystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion Deposited 2018-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa） Fragment：residues 230-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；bis-tris propane 5 mM sodium chloride 100 mM 1-propanol 14% spermidine-HCl 5 mM dithiothreitol 5 mM	Resolution 3.36 Å R-free 0.268
6UBF Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol	Resolution 4.60 Å R-free 0.356
6UG1 Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 256–311（56 aa） Fragment：UNP residues 256-311	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride	Resolution 2.83 Å R-free 0.272
6UIN Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa） Fragment：UNP residues 230-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 200 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride	Resolution 3.35 Å R-free 0.262

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAD23_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–72； UniProt 238–309

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1x3w
Deposition date deposition_date	2005-05-11
Structure title title	Structure of a peptide:N-glycanase-Rad23 complex
Keywords keywords	Protein-protein complex, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.40 Å
Radius of gyration Rg (electron density) rg_electron	24.56 Å
Forward intensity I(0) i0	35295200.00
Molecular weight molecular_weight	45366.0 kDa
Excluded volume excluded_volume	56420 Å³
Envelope volume envelope_volume	67477 Å³
Hydration-shell volume shell_volume	24391 Å³
Envelope diameter envelope_diameter	95.6 Å
Shell Rg shell_rg	30.12 Å
Envelope Rg envelope_rg	24.82 Å
Shape Rg shape_rg	24.43 Å
Total Rg total_rg	25.61 Å
Total atoms total_atoms	3170
Residues n_residues	372
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	92.7 Å
Rg (real space) rg_real	25.57 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	3.5300e+07
I(0) uncertainty (real space) i0_real_error	5.7310e+05
Rg (reciprocal space) rg_reciprocal	25.52 Å
I(0) (reciprocal space) i0_reciprocal	35290000.0000
Solution quality estimate total_estimate	0.8286
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.4 Å
Skewness Skewness skewness	0.625
Kurtosis Kurtosis kurtosis	0.295
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4554000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.874; Smooth: 0.931

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	peptide:N-glycanase
Molecular weight formula_weight	39566.2 kDa
EC 编号 ec_number	3.5.1.52
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3187

NNIDFDSIAKMLLIKYKDFILSKFKKAAPVENIRFQNLVHTNQFAQGVLGQSQHLCTVYDNPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTDYLVKELLRYFKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPRYNDPIKLLETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFDQPYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQNELPRDQIKEEDLKFLCQFITKRLRYSLNDDEIYQLACRDEQEQIELIRGKTQETKSESVSAASKS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	UV excision repair protein RAD23
Molecular weight formula_weight	7539.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GTTGGATDAAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEAV

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1x3wa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.4 — Transglutaminase core

Domain ID domain_id	d1x3wb1
Class class	a — All alpha proteins
Fold Fold fold	a.189 — XPC-binding domain-like
Superfamily Superfamily superfamily	a.189.1 — XPC-binding domain
Family Family family	a.189.1.1 — XPC-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id	1x3wA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	270 —

Domain ID domain_id	1x3wA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1x3wA04
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1x3wB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	540 — XPC-binding domain

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8. Citations (1)

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Unit-cell length a length_a	129.235 Å
Unit-cell length b length_b	129.235 Å
Unit-cell length c length_c	128.494 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2452
R_work r_work	0.2437
R_free r_free	0.2742

fit	/app/data/saxs_computation/x3/1x3w/1x3w.fit
pddf	/app/data/pr_computation/x3/1x3w/1x3w.pr.out
profile	/app/data/saxs_computation/x3/1x3w/1x3w.dat

Structure of a peptide:N-glycanase-Rad23 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

peptide:N-glycanase

State in the Current Structure

Other States of the Same Protein in the Database

UV excision repair protein RAD23

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)