8CGQ | pdb_00008cgq

Crystal structure of UGT708A6 with UDP

PDB DOI: https://doi.org/10.2210/pdb8CGQ/pdb

Classification: TRANSFERASE
Organism(s): Zea mays
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-06 Released: 2024-02-21
Deposition Author(s): Fredslund, F., Bidart, G.N., Welner, D.H.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.179 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of UGT708A6 with UDP

Fredslund, F., Bidart, G.N., Welner, D.H.

To be published.

Macromolecule Content

Total Structure Weight: 51.16 kDa
Atom Count: 3,625
Modeled Residue Count: 458
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glycosyltransferase 708A6	A	476	Zea mays	Mutation(s): 0 Gene Names: UGT708A6 EC: 2.4.1
UniProt
Find proteins for A0A096SRM5 (Zea mays) Explore A0A096SRM5 Go to UniProtKB: A0A096SRM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A096SRM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL (Subject of Investigation/LOI) Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.227 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.179 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.431	α = 90
b = 72.593	β = 101.694
c = 57.018	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF20CC0035580

Revision History (Full details and data files)

Version 1.0: 2024-02-21
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.