5L0V

human POGLUT1 in complex with 2F-glucose modified EGF(+) and UDP

• PDB DOI: https://doi.org/10.2210/pdb5L0V/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-28 Released: 2017-08-09 
• Deposition Author(s): Li, Z., Rini, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.96 kDa 
• Atom Count: 3,933 
• Modelled Residue Count: 396 
• Deposited Residue Count: 399 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-glucosyltransferase 1	A	357	Homo sapiens	Mutation(s): 0  Gene Names: POGLUT1, C3orf9, CLP46, KTELC1, MDSRP, MDS010, UNQ490/PRO1006 EC: 2.4.1 (PDB Primary Data), 2.4.2.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBL1 (Homo sapiens) Explore Q8NBL1  Go to UniProtKB:  Q8NBL1
PHAROS:  Q8NBL1 GTEx:  ENSG00000163389

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EGF(+)	B	42	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	G [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SHG	J [auth B]	2-deoxy-2-fluoro-beta-D-glucopyranose C6 H11 F O5 ZCXUVYAZINUVJD-QZABAPFNSA-N
MPD	H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.81	α = 90
b = 74.89	β = 90
c = 83.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Li, Z., Rini, J.M.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references
• Version 1.2: 2018-04-18
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-03-24
  Changes: Source and taxonomy, Structure summary