6FSN | pdb_00006fsn

Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP-glucose (conformation 1)

PDB DOI: https://doi.org/10.2210/pdb6FSN/pdb

Classification: TRANSFERASE
Organism(s): Thermochaetoides thermophila
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-02-19 Released: 2019-03-20
Deposition Author(s): Roversi, P., Le Cornu, J.D., Hill, J., Alonzi, D.S., Zitzmann, N.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.227 (Depositor), 0.232 (DCC)
R-Value Work:
0.211 (Depositor), 0.215 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal polymorphism in fragment-based lead discovery of ligands of the catalytic domain of UGGT, the glycoprotein folding quality control checkpoint.

Caputo, A.T., Ibba, R., Le Cornu, J.D., Darlot, B., Hensen, M., Lipp, C.B., Marciano, G., Vasiljevic, S., Zitzmann, N., Roversi, P.

(2022) Front Mol Biosci

DOI: https://doi.org/10.3389/fmolb.2022.960248

Macromolecule Content

Total Structure Weight: 36.53 kDa
Atom Count: 2,743
Modeled Residue Count: 276
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose-glycoprotein glucosyltransferase-like protein	A	299	Thermochaetoides thermophila	Mutation(s): 0 Gene Names: CTHT_0048990
UniProt
Find proteins for G0SB58 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SB58 Go to UniProtKB: G0SB58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SB58
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG (Subject of Investigation/LOI) Query on UPG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA (Subject of Investigation/LOI) Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free: 0.227 (Depositor), 0.232 (DCC)
R-Value Work: 0.211 (Depositor), 0.215 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.832	α = 90
b = 118.832	β = 90
c = 68.754	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106272/Z/14/Z

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2020-07-08
Changes: Data collection
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary
Version 1.3: 2022-11-30
Changes: Database references, Structure summary
Version 1.4: 2022-12-21
Changes: Database references
Version 1.5: 2024-01-31
Changes: Data collection, Refinement description
Version 1.6: 2024-10-16
Changes: Structure summary