5M79

Blood group synthase AAGlyB in complex with UMP and cryoprotected with glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Blood group synthase AAGlyB in complex with UMP and cryoprotected with glycerol

Rocha, J.Batot, G.O.Palcic, M.M.Breton, C.Royant, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histo-blood group ABO system transferase298Homo sapiensMutation(s): 2 
Gene Names: ABO
EC: 2.4.1.40 (PDB Primary Data), 2.4.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P16442 (Homo sapiens)
Explore P16442 
Go to UniProtKB:  P16442
PHAROS:  P16442
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16442
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download Ideal Coordinates CCD File 
C [auth A]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.606α = 90
b = 148.717β = 90
c = 79.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-BSV8-0011-02

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description