6ej7

Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG

Method: X-RAY DIFFRACTION D_max: 94.1 Å Quality: EXCELLENT

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

Xylosyltransferase 1

Homo sapiens

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	Not recorded	Protein AMBP × 1 （P02760） 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

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 6EJ7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6EJ8 Human Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG 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）	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 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	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 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） 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 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） 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 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） 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 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） 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
6EJE Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT 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） 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 2.43 Å R-free 0.235
6FOA Human Xylosyltransferase 1 apo structure Deposited 2018-02-06	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

Protein AMBP

OrganismNot specified

UniProt P02760

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 210–221	Mutation：S215A, L220G, V221G	Xylosyltransferase 1 × 1 （Q86Y38） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6EJ7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BIK X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR COMPLEX Deposited 1997-11-26	Different construct Different mutation/modification 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 206–352（147 aa） Fragment：DOMAIN II,78 - 133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.253
3QKG Crystal structure of alpha-1-microglobulin at 2.3 A resolution Deposited 2011-02-01	Different construct Different mutation/modification 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 20–202（183 aa） Fragment：lipocalin	Mutation：C34S	NI NICKEL (II) ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100 mM Tris-HCl, 1.1 M sodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.260
4ES7 crystal structure of protein HC from Homo sapiens at 2 angstrom Deposited 2012-04-22	Different construct Different mutation/modification 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 27–193（167 aa） Fragment：UNP residues 27-193	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；0.2M ammonium citrate, 20% PEG 3350, 0.1M HEPES pH 6.9, 40% 1,1,1,3,3,3-Hexafluoro-z-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.261
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	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 X 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
4U30 Human mesotrypsin complexed with bikunin Kunitz domain 2 Deposited 2014-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 283–340（58 aa） Fragment：BPTI/Kunitz inhibitor 2 residues 285-338	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.0 and 1 M sodium citrate	Resolution 2.50 Å R-free 0.223
6EJ8 Human Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG Deposited 2017-09-20	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 210–221（12 aa）	Mutation：L220G, V221G	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–220（11 aa）	Mutation：E212P, L220G, V221G	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 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 210–221（12 aa） Fragment：UNP residues 210-221	Mutation：G214Y, L220G, V221G	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 210–221（12 aa）	Mutation：G216A, L220G, V221G	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 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 210–221（12 aa） Fragment：UNP residues 210-221	Mutation：G217V, L220G, V221G	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 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 210–221（12 aa） Fragment：UNP residues 210-221	Mutation：G218P, L220G, V221G	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

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

View Construct and Data Evidence

UniProt name	AMBP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 210–221

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ej7
Deposition date deposition_date	2017-09-20
Structure title title	Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG
Keywords keywords	Proteoglycan, Glycosyltransferase, Golgi, Xylosyltransferase, TRANSFERASE; TRANSFERASE
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	29.45 Å
Radius of gyration Rg (electron density) rg_electron	28.65 Å
Forward intensity I(0) i0	115430000.00
Molecular weight molecular_weight	82965.0 kDa
Excluded volume excluded_volume	102930 Å³
Envelope volume envelope_volume	129340 Å³
Hydration-shell volume shell_volume	37045 Å³
Envelope diameter envelope_diameter	102.2 Å
Shell Rg shell_rg	36.54 Å
Envelope Rg envelope_rg	28.74 Å
Shape Rg shape_rg	28.63 Å
Total Rg total_rg	29.46 Å
Total atoms total_atoms	11390
Residues n_residues	716
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	94.1 Å
Rg (real space) rg_real	29.36 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	1.1540e+08
I(0) uncertainty (real space) i0_real_error	1.6550e+06
Rg (reciprocal space) rg_reciprocal	29.40 Å
I(0) (reciprocal space) i0_reciprocal	115400000.0000
Solution quality estimate total_estimate	0.9031
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.234
Kurtosis Kurtosis kurtosis	-0.479
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17530000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Xylosyltransferase 1
Molecular weight formula_weight	86122.0 kDa
EC 编号 ec_number	2.4.2.26
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	11801

APLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Protein AMBP
Molecular weight formula_weight	1075.0 kDa
Mutation mutation	S215A, L220G, V221G
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QEEEGAGGGQGG

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
Molecular weight formula_weight	536.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	366

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8. Citations (1)

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Unit-cell length a length_a	67.460 Å
Unit-cell length b length_b	86.890 Å
Unit-cell length c length_c	152.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	76.455 Å
R factor r_factor	0.2001
R_work r_work	0.1985
R_free r_free	0.2298

fit	/app/data/saxs_computation/ej/6ej7/6ej7.fit
pddf	/app/data/pr_computation/ej/6ej7/6ej7.pr.out
profile	/app/data/saxs_computation/ej/6ej7/6ej7.dat

Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG

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

Xylosyltransferase 1

State in the Current Structure

Other States of the Same Protein in the Database

Protein AMBP

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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)