7SCD

Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-1 octasaccharide substrate and co-factor product PAP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history. 


Literature

Structural and Substrate Specificity Analysis of 3-O-Sulfotransferase Isoform 5 to Synthesize Heparan Sulfate

Wander, R., Kaminski, A.M., Wang, Z., Stancanelli, E., Xu, Y., Pagadala, V., Li, J., Krahn, J.M., Pham, T.Q., Liu, J., Pedersen, L.C.

(2021) ACS Catal 11: 14956-14966


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin 1,Heparan sulfate glucosamine 3-O-sulfotransferase 5372Escherichia coli K-12, Homo sapiens
This entity is chimeric		Mutation(s): 1 
Gene Names: trxA, fipA, tsnC, b3781, JW5856, HS3ST5, 3OST5, HS3OST5
EC: 2.8.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P0AA25 (Escherichia coli (strain K12))
Explore P0AA25 
Go to UniProtKB:  P0AA25
Find proteins for Q8IZT8 (Homo sapiens)
Explore Q8IZT8 
Go to UniProtKB:  Q8IZT8
PHAROS:  Q8IZT8
GTEx:  ENSG00000249853 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AA25Q8IZT8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acidB [auth C]6N/A
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3P (Subject of Investigation/LOI)
Query on A3P
Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.84α = 90
b = 58.82β = 90
c = 153.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIA-ES102645
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL094463
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL144970
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128484
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134738
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL139197

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary