7SCE | pdb_00007sce

Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-2 octasaccharide substrate and co-factor product PAP

• PDB DOI: https://doi.org/10.2210/pdb7SCE/pdb

• Classification: TRANSFERASE/SUBSTRATE
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-09-27 Released: 2022-01-19 
• Deposition Author(s): Wander, R., Kaminski, A.M., Krahn, J.M., Liu, J., Pedersen, L.C.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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

• DOI: https://doi.org/10.1021/acscatal.1c04520

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.84 kDa 
• Atom Count: 3,060 
• Modeled Residue Count: 370 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 1,Heparan sulfate glucosamine 3-O-sulfotransferase 5	A	372	Escherichia 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
UniProt Groups	P0AA25Q8IZT8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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)-2-O-sulfo-alpha-L-idopyranuronic acid	B [auth C]	6		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P (Subject of Investigation/LOI)	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: 2.75 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.421	α = 90
b = 58.997	β = 90
c = 151.045	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Wander, R., Kaminski, A.M., Krahn, J.M., Liu, J., Pedersen, L.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIA-ES102645
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL094463
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL144970
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM128484
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM134738
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL139197

Revision History  

• Version 1.0: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary