6GQD | pdb_00006gqd

Structure of human galactose-1-phosphate uridylyltransferase (GALT), with crystallization epitope mutations A21Y:A22T:T23P:R25L

PDB DOI: https://doi.org/10.2210/pdb6GQD/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-07 Released: 2018-07-18
Deposition Author(s): Fairhead, M., Strain-Damerell, C., Kopec, J., Bezerra, G.A., Zhang, M., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.188 (Depositor), 0.193 (DCC)
R-Value Work:
0.162 (Depositor), 0.167 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6GQD

Ligand Structure Quality Assessment

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

Literature

Structure of human galactose-1-phosphate uridylyltransferase (GALT), with crystallization epitope mutations A21Y:A22T:T23P:R25L

Fairhead, M., Strain-Damerell, C., Kopec, J., Bezerra, G.A., Zhang, M., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 44.1 kDa
Atom Count: 3,269
Modeled Residue Count: 344
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-1-phosphate uridylyltransferase	A	380	Homo sapiens	Mutation(s): 0 Gene Names: GALT EC: 2.7.7.12
UniProt & NIH Common Fund Data Resources
Find proteins for P07902 (Homo sapiens) Explore P07902 Go to UniProtKB: P07902
PHAROS: P07902 GTEx: ENSG00000213930
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07902
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H2U Query on H2U Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE C₉ H₁₅ N₂ O₉ P NBWDKGJHOHJBRJ-XVFCMESISA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.188 (Depositor), 0.193 (DCC)
R-Value Work: 0.162 (Depositor), 0.167 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.647	α = 90
b = 96.748	β = 90
c = 55.426	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Strain-Damerell, C.

Burgess-Brown, N.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106169/ZZ14/Z

Revision History (Full details and data files)

Version 1.0: 2018-07-18
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

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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.