1T8U

Crystal Structure of human 3-O-Sulfotransferase-3 with bound PAP and tetrasaccharide substrate

• PDB DOI: https://doi.org/10.2210/pdb1T8U/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-13 Released: 2004-08-31 
• Deposition Author(s): Moon, A.F., Edavettal, S.C., Krahn, J.M., Munoz, E.M., Negishi, M., Linhardt, R.J., Liu, J., Pedersen, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.222 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.41 kDa 
• Atom Count: 4,828 
• Modelled Residue Count: 539 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1	A, B	272	Homo sapiens	Mutation(s): 0  Gene Names: h3-OST-3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y663 (Homo sapiens) Explore Q9Y663  Go to UniProtKB:  Q9Y663
PHAROS:  Q9Y663 GTEx:  ENSG00000153976

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan:  G88016IC GlyCosmos:  G88016IC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	G [auth B], H [auth B]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	E [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.222 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.806	α = 90
b = 154.525	β = 90
c = 91.931	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-31 
Deposition Author(s): Moon, A.F., Edavettal, S.C., Krahn, J.M., Munoz, E.M., Negishi, M., Linhardt, R.J., Liu, J., Pedersen, L.C.

Revision History  

• Version 1.0: 2004-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description, Structure summary