6Z2F

Crystal structure of human AGX1 mutant complexed with UDPGLCNAC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of human AGX1 mutant complexed with UDPGLCNAC

Chen, X.van Aalten, D.M.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylhexosamine pyrophosphorylase509Homo sapiensMutation(s): 1 
Gene Names: UAP1SPAG2
EC: 2.7.7.83 (PDB Primary Data), 2.7.7.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16222 (Homo sapiens)
Explore Q16222 
Go to UniProtKB:  Q16222
PHAROS:  Q16222
GTEx:  ENSG00000117143 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16222
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylhexosamine pyrophosphorylase509Homo sapiensMutation(s): 1 
Gene Names: UAP1SPAG2
EC: 2.7.7.83 (PDB Primary Data), 2.7.7.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16222 (Homo sapiens)
Explore Q16222 
Go to UniProtKB:  Q16222
PHAROS:  Q16222
GTEx:  ENSG00000117143 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16222
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UD1
Query on UD1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
B
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.614α = 95.63
b = 64.569β = 101.09
c = 82.07γ = 104.93
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description