2B69

Crystal Structure of Human UDP-glucoronic acid decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb2B69/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-09-30 Released: 2005-10-18 
• Deposition Author(s): Ugochukwu, E., Dubinina, E., Kavanagh, K., Sundstrom, M., Weigelt, J., Edwards, A., Arrowsmith, C., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.162 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 

Literature

Crystal Structure of Human UDP-glucoronic acid decarboxylase

Ugochukwu, E., Dubinina, E., Kavanagh, K., Sundstrom, M., Weigelt, J., Edwards, A., Arrowsmith, C., von Delft, F., Oppermann, U.

To be published.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 40.68 kDa 
• Atom Count: 2,952 
• Modelled Residue Count: 312 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucuronate decarboxylase 1	A	343	Homo sapiens	Mutation(s): 10  Gene Names: UXS1 EC: 4.1.1.35
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBZ7 (Homo sapiens) Explore Q8NBZ7  Go to UniProtKB:  Q8NBZ7
PHAROS:  Q8NBZ7 GTEx:  ENSG00000115652

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UDP	C [auth A], D [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.162 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46	α = 90
b = 45	β = 97
c = 85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-18 
Deposition Author(s): Ugochukwu, E., Dubinina, E., Kavanagh, K., Sundstrom, M., Weigelt, J., Edwards, A., Arrowsmith, C., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2005-10-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary