4NDZ

Structure of Maltose Binding Protein fusion to 2-O-Sulfotransferase with bound heptasaccharide and PAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Deciphering the role of 2-O-sulfotransferase in regulating heparan sulfate biosynthesis

Liu, C.Sheng, J.Krahn, J.M.Perera, L.Xu, Y.Hsieh, P.Liu, J.Pedersen, L.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1 fusion
A, B, C, D, E
A, B, C, D, E, F
658Escherichia coli UMEA 3304-1Gallus gallus
This entity is chimeric
Mutation(s): 4 
Gene Names: G962_03763HS2ST1HS2ST
EC: 2.8.2
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q76KB1 (Gallus gallus)
Explore Q76KB1 
Go to UniProtKB:  Q76KB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q76KB1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid
G, I, L, N, P
7N/A
Glycosylation Resources
GlyTouCan:  G54413LX
GlyCosmos:  G54413LX
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
H, J, K, M, O
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P

Download Ideal Coordinates CCD File 
Q [auth A]
S [auth B]
U [auth C]
V [auth D]
X [auth E]
Q [auth A],
S [auth B],
U [auth C],
V [auth D],
X [auth E],
Z [auth F]
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
NPO
Query on NPO

Download Ideal Coordinates CCD File 
R [auth A],
T [auth B],
W [auth D],
Y [auth E]
P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.72α = 90
b = 170.69β = 90
c = 183.96γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary