7C2X | pdb_00007c2x

Crystal Structure of Glycyrrhiza uralensis UGT73P12 complexed with glycyrrhetinic acid 3-O-monoglucuronide

PDB DOI: https://doi.org/10.2210/pdb7C2X/pdb

Classification: TRANSFERASE
Organism(s): Glycyrrhiza uralensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-05-09 Released: 2021-05-12
Deposition Author(s): Ren, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.183 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of Glycyrrhiza uralensis UGT73P12 complexed with glycyrrhetinic acid 3-O-monoglucuronide

Ren, J., Liu, M.

To be published.

Macromolecule Content

Total Structure Weight: 58.89 kDa
Atom Count: 4,263
Modeled Residue Count: 490
Deposited Residue Count: 514
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	514	Glycyrrhiza uralensis	Mutation(s): 0 Gene Names: UGT73P12 EC: 2.4.1
UniProt
Find proteins for A0A5A4WN00 (Glycyrrhiza uralensis) Explore A0A5A4WN00 Go to UniProtKB: A0A5A4WN00
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5A4WN00
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FJL (Subject of Investigation/LOI) Query on FJL 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]	(2~{S},3~{S},4~{S},5~{R},6~{R})-6-[[(3~{S},4~{a}~{R},6~{a}~{R},6~{b}~{S},8~{a}~{S},11~{S},12~{a}~{R},14~{a}~{R},14~{b}~{S})-11-carboxy-4,4,6~{a},6~{b},8~{a},11,14~{b}-heptamethyl-14-oxidanylidene-2,3,4~{a},5,6,7,8,9,10,12,12~{a},14~{a}-dodecahydro-1~{H}-picen-3-yl]oxy]-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid C₃₆ H₅₄ O₁₀ HLDYLAJAWSKPFZ-QDPIGISRSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UDP Query on UDP 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]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.183 (Depositor), 0.184 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.465	α = 90
b = 84.425	β = 90
c = 92.836	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MrBUMP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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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.