← Back to search
6eje

Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT

Method: X-RAY DIFFRACTION Dmax: 93.2 Å Quality: EXCELLENT
▼

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

Xylosyltransferase 1

Homo sapiens

UniProt Q86Y38

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 232–959 Fragment：UNP residues 232-959 Syndecan-1 × 1 （P18827） PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each) Resolution 2.43 Å R-free 0.235

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 6EJE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6EJ7 Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG Deposited 2017-09-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 232–959（728 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 1 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 9 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus precipitant mix 2 (PEG8000 and ethylene glycol), 0.1M Bicine/Tris buffer at pH 7.5 0.1 M of Morpheus NPS mix.
Resolution 2.00 Å R-free 0.230
6EJ8 Human Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG Deposited 2017-09-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 232–959（728 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)
Resolution 2.09 Å R-free 0.223
6EJ9 Human Xylosyltransferase 1 in complex with peptide QEPEGSGGGQGG Deposited 2017-09-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 232–959（728 aa）
Not recorded PO4 PHOSPHATE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)
Resolution 2.02 Å R-free 0.225
6EJA Human Xylosyltransferase 1 in complex with peptide QEEEYSGGGQGG Deposited 2017-09-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 232–959（728 aa） Fragment：UNP residues 232-959
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)
Resolution 1.94 Å R-free 0.212
6EJB Human Xylosyltransferase 1 in complex with peptide QEEEGSAGGQGG Deposited 2017-09-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 232–959（728 aa） Fragment：UNP residues 232-959
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)
Resolution 2.56 Å R-free 0.280
6EJC Human Xylosyltransferase 1 in complex with peptide QEEEGSGVGQGG Deposited 2017-09-20 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 232–959（728 aa） Fragment：UNP residues 232-959
Not recorded PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)
Resolution 2.06 Å R-free 0.273
6EJD Human Xylosyltransferase 1 in complex with peptide QEEEGSGGPQGG Deposited 2017-09-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 232–959（728 aa） Fragment：UNP residues 232-959
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)
Resolution 2.68 Å R-free 0.279
6FOA Human Xylosyltransferase 1 apo structure Deposited 2018-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 232–959（728 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% precipitant mix 2 (PEG8000 and ethylene glycol), 100 mM Bicine/Tris buffer at pH 7.5 100 mM of a sodium nitrate/sodium phosphate/ammonium sulphate mix.
Resolution 1.87 Å R-free 0.222

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XYLT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 24–751； UniProt 232–959

Syndecan-1

OrganismNot specified

UniProt P18827

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 201–212 Fragment：UNP residues 201-212 Xylosyltransferase 1 × 1 （Q86Y38） PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each) Resolution 2.43 Å R-free 0.235

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 6EJE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GVC Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with phosphorylated Syndecan1 Peptide Deposited 2012-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 303–310（8 aa） Fragment：UNP residues 303-310
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1 M sodium acetate, 25% PEG4000, 8% isopropanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.54 Å R-free 0.200
4GVD Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide Deposited 2012-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 303–310（8 aa） Fragment：UNP residues 303-310
Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 1 ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1 M MES, 20% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.85 Å R-free 0.243
4GVD Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide Deposited 2012-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 303–310（8 aa） Fragment：UNP residues 303-310
Not recorded CL CHLORIDE ION × 1 NA SODIUM ION × 1 ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1 M MES, 20% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.85 Å R-free 0.243

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SDC1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–12； UniProt 201–212

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6eje

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6eje
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6eje
Deposition date deposition_date2017-09-20
Structure title titleHuman Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT
Keywords keywordsProteoglycan, Glycosyltransferase, Golgi, Xylosyltransferase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.32 Å
Radius of gyration Rg (electron density) rg_electron28.46 Å
Forward intensity I(0) i0100113000.00
Molecular weight molecular_weight78933.0 kDa
Excluded volume excluded_volume98690 ų
Envelope volume envelope_volume123300 ų
Hydration-shell volume shell_volume35793 ų
Envelope diameter envelope_diameter99.1 Å
Shell Rg shell_rg36.14 Å
Envelope Rg envelope_rg28.39 Å
Shape Rg shape_rg28.42 Å
Total Rg total_rg29.30 Å
Total atoms total_atoms10880
Residues n_residues704
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax93.2 Å
Rg (real space) rg_real29.24 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real1.0010e+08
I(0) uncertainty (real space) i0_real_error1.6140e+06
Rg (reciprocal space) rg_reciprocal29.28 Å
I(0) (reciprocal space) i0_reciprocal100100000.0000
Solution quality estimate total_estimate0.9070
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.5 Å
Skewness Skewness skewness0.225
Kurtosis Kurtosis kurtosis-0.493
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16200000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.985
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (1)

▶

9. Files and Curves (10)