6Q4M | pdb_00006q4m

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation

PDB DOI: https://doi.org/10.2210/pdb6Q4M/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-12-06 Released: 2019-12-25
Deposition Author(s): Gundogdu, M., van Aalten, D.M.F.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.199 (Depositor), 0.202 (DCC)
R-Value Work:
0.175 (Depositor), 0.181 (DCC)
R-Value Observed:
0.176 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation

Gundogdu, M., van Aalten, D.M.F.

To be published.

Macromolecule Content

Total Structure Weight: 81.84 kDa
Atom Count: 5,948
Modeled Residue Count: 698
Deposited Residue Count: 723
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A	723	Homo sapiens	Mutation(s): 1 Gene Names: OGT EC: 2.4.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens) Explore O15294 Go to UniProtKB: O15294
PHAROS: O15294 GTEx: ENSG00000147162
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15294
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12V Query on 12V 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]	(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate C₁₇ H₂₇ N₃ O₁₆ P₂ S JPRVHSQHWXZSNC-UBDZBXRQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		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: 2.20 Å
R-Value Free: 0.199 (Depositor), 0.202 (DCC)
R-Value Work: 0.175 (Depositor), 0.181 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.316	α = 90
b = 150.736	β = 90
c = 199.492	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

van Aalten, D.M.F.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	110061

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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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.