4HO9

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP

PDB DOI: https://doi.org/10.2210/pdb4HO9/pdb

Classification: TRANSFERASE
Organism(s): Aneurinibacillus thermoaerophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-22 Released: 2013-10-23
Deposition Author(s): Chen, T.J., Chien, W.T., Lin, C.C., Wang, W.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.211
R-Value Work: 0.171
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP

Chen, T.J., Chien, W.T., Lin, C.C., Wang, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 68.91 kDa
Atom Count: 5,253
Modelled Residue Count: 582
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A, B	297	Aneurinibacillus thermoaerophilus	Mutation(s): 0 Gene Names: rmlA EC: 2.7.7.24
UniProt
Find proteins for Q9AGY4 (Aneurinibacillus thermoaerophilus) Explore Q9AGY4 Go to UniProtKB: Q9AGY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9AGY4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDU Query on GDU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-ABVWGUQPSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
UTP Query on UTP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	URIDINE 5'-TRIPHOSPHATE C₉ H₁₅ N₂ O₁₅ P₃ PGAVKCOVUIYSFO-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.211
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 114.788	α = 90
b = 90.763	β = 125.2
c = 87.702	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4HO9

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)