1GA8

CRYSTAL STRUCTURE OF GALACOSYLTRANSFERASE LGTC IN COMPLEX WITH DONOR AND ACCEPTOR SUGAR ANALOGS.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GALACTOSYL TRANSFERASE LGTC311Neisseria meningitidisMutation(s): 9 
Gene Names: LGTC
EC: 2.4.1.44
UniProt
Find proteins for Q93EK7 (Neisseria meningitidis)
Explore Q93EK7 
Go to UniProtKB:  Q93EK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93EK7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-beta-D-xylo-hexopyranose-(1-4)-beta-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G86561HH
GlyCosmos:  G86561HH
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UPF
Query on UPF
Download Ideal Coordinates CCD File 
D [auth A]URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-KBQKSTHMSA-N
MN
Query on MN
Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
UPF Binding MOAD:  1GA8 Ki: 2000 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.975α = 90
b = 76.158β = 90
c = 87.228γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Advisory, Database references, Structure summary
  • Version 2.2: 2023-08-09
    Changes: Data collection, Refinement description
  • Version 2.3: 2023-11-15
    Changes: Data collection