2B69 | pdb_00002b69

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free:
0.162 (Depositor), 0.136 (DCC)
R-Value Work:
0.134 (Depositor), 0.139 (DCC)
R-Value Observed:
0.136 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.136 (DCC)
R-Value Work: 0.134 (Depositor), 0.139 (DCC)
R-Value Observed: 0.136 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-10-18

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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