5ZES | pdb_00005zes

UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - UDP complex

PDB DOI: https://doi.org/10.2210/pdb5ZES/pdb

Classification: TRANSFERASE
Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-27 Released: 2019-03-06
Deposition Author(s): Killivalavan, A., Lee, K.H.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.235 (Depositor), 0.241 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZES

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - UDP complex

Killivalavan, A., Lee, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 77.09 kDa
Atom Count: 5,576
Modeled Residue Count: 705
Deposited Residue Count: 706
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose:tetrahydrobiopterin glucosyltransferase	A, B	353	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0
UniProt
Find proteins for Q31LX1 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31LX1 Go to UniProtKB: Q31LX1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q31LX1
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]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.235 (Depositor), 0.241 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.81	α = 90
b = 78.698	β = 90.87
c = 53.605	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-06

Deposition Author(s):

Killivalavan, A.

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2012R1A1A2044394

Revision History (Full details and data files)

Version 1.0: 2019-03-06
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.