8B68 | pdb_00008b68

Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070 in complex with UDP-glucose

PDB DOI: https://doi.org/10.2210/pdb8B68/pdb

Classification: TRANSFERASE
Organism(s): Thermocrispum agreste DSM 44070
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-26 Released: 2024-01-10
Deposition Author(s): Laustsen, J.U., Bento, I.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.204 (Depositor), 0.206 (DCC)
R-Value Work:
0.176 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure determination of a highly active UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070

Kumpf, A., Maier, A., Laustsen, J.U., Jeffries, C.M., Bento, I., Tischler, D.

To be published.

Macromolecule Content

Total Structure Weight: 66.57 kDa
Atom Count: 5,136
Modeled Residue Count: 575
Deposited Residue Count: 598
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	A, B	299	Thermocrispum agreste DSM 44070	Mutation(s): 0 Gene Names: DIU77_00305 EC: 2.7.7.9
UniProt
Find proteins for A0A2W4LV58 (Thermocrispum agreste) Explore A0A2W4LV58 Go to UniProtKB: A0A2W4LV58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2W4LV58
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain H [auth A] SDF format, chain R [auth A] SDF format, chain W [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain R [auth A] mmCIF format, chain W [auth B]	AA [auth B], H [auth A], R [auth A], W [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain H [auth A] Focus chain R [auth A] Focus chain W [auth B] Interactions & Density Focus chain AA [auth B] Focus chain H [auth A] Focus chain R [auth A] Focus chain W [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	BA [auth B] CA [auth B] D [auth A] E [auth A] F [auth A] BA [auth B], CA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth A], U [auth A], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain U [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain U [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]