RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Citation Author = "Thymark, M."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 26 Structures.

Refinements

Structure Determination Methodology

experimental (26)

Scientific Name of Source Organism

	Escherichia coli (6)
	Saccharolobus solfataricus (5)
	Bacillus subtilis (3)
	Methanocaldococcus jannaschii (3)
	Mycobacterium tuberculosis H37Rv (3)
	synthetic construct (3)
	Hordeum vulgare (2)
	Halalkalibacterium halodurans C-125 (1)

Taxonomy

	Bacteria (13)
	Archaea (8)
	other sequences (3)
	Eukaryota (2)

Experimental Method

X-RAY DIFFRACTION (26)

Polymer Entity Type

Protein (26)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (10)
	2.5 - 3.0 (11)
	3.0 - 3.5 (1)

Release Date

	2000 - 2004 (6)
	2005 - 2009 (14)
	2010 - 2014 (2)
	2015 - 2019 (2)
	2020 - 2024 (2)

Enzyme Classification Name

	Hydrolases (22)
	Transferases (2)
	Ligases (1)

Symmetry Type

	Cyclic (12)
	Dihedral (14)
	Asymmetric (5)
	Octahedral (1)

SCOP Classification

	All beta proteins (17)
	Alpha and beta proteins (a/b) (9)
	Artifacts (2)

AllSelected

1 to 25 of 26 Structures

Page 1 of 2

Sort by

Explore in 3D

1UWZ \| pdb_00001uwz	Download File View File

Bacillus subtilis cytidine deaminase with an Arg56 - Ala substitution

Johansson, E., Neuhard, J., Willemoes, M., Larsen, S.

(2004) Biochemistry 43: 6020

Released	2004-05-20
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Bacillus subtilis
Macromolecule	CYTIDINE DEAMINASE (protein)
Unique Ligands	THU, ZN

Explore in 3D

1UX0 \| pdb_00001ux0	Download File View File

Bacillus subtilis cytidine deaminase with an Arg56 - Gln substitution

Johansson, E., Neuhard, J., Willemoes, M., Larsen, S.

(2004) Biochemistry 43: 6020

Released	2004-05-20
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Bacillus subtilis
Macromolecule	CYTIDINE DEAMINASE (protein)
Unique Ligands	THU, ZN

Explore in 3D

1UX1 \| pdb_00001ux1	Download File View File

Bacillus subtilis cytidine deaminase with a Cys53His and an Arg56Gln substitution

Johansson, E., Neuhard, J., Willemoes, M., Larsen, S.

(2004) Biochemistry 43: 6020

Released	2004-05-20
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Bacillus subtilis
Macromolecule	CYTIDINE DEAMINASE (protein)
Unique Ligands	THU, TRS, ZN

Explore in 3D

1VST \| pdb_00001vst	Download File View File

Symmetric Sulfolobus solfataricus uracil phosphoribosyltransferase with bound PRPP and GTP

Kadziola, A.

(2009) J Mol Biology 393: 464-477

Released	2009-09-01
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Uracil phosphoribosyltransferase (protein)
Unique Ligands	GTP, MG, PRP

Explore in 3D

1XS1 \| pdb_00001xs1	Download File View File

dCTP deaminase from Escherichia coli in complex with dUTP

Johansson, E., Fano, M., Bynck, J.H., Neuhard, J., Larsen, S., Sigurskjold, B.W., Christensen, U., Willemoes, M.

(2005) J Biological Chem 280: 3051-3059

Released	2004-12-21
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	Deoxycytidine triphosphate deaminase (protein)
Unique Ligands	DUT, MG

Explore in 3D

1XS4 \| pdb_00001xs4	Download File View File

dCTP deaminase from Escherichia coli- E138A mutant enzyme in complex with dCTP

Johansson, E., Fano, M., Bynck, J.H., Neuhard, J., Larsen, S., Sigurskjold, B.W., Christensen, U., Willemoes, M.

(2005) J Biological Chem 280: 3051-3059

Released	2004-12-21
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	Escherichia coli
Macromolecule	Deoxycytidine triphosphate deaminase (protein)
Unique Ligands	DCP, MG

Explore in 3D

1XS6 \| pdb_00001xs6	Download File View File

dCTP deaminase from Escherichia coli. E138A mutant enzyme in complex with dUTP

Johansson, E., Fano, M., Bynck, J.H., Neuhard, J., Larsen, S., Sigurskjold, B.W., Christensen, U., Willemoes, M.

(2005) J Biological Chem 280: 3051-3059

Released	2004-12-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	Deoxycytidine triphosphate deaminase (protein)
Unique Ligands	DUT, MG

Explore in 3D

2G3M \| pdb_00002g3m	Download File View File

Crystal structure of the Sulfolobus solfataricus alpha-glucosidase MalA

Ernst, H.A., Lo Leggio, L., Willemoes, M., Leonard, G., Blum, P., Larsen, S.

(2006) J Mol Biology 358: 1106-1124

Released	2006-05-02
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Alpha-glucosidase (protein)

Explore in 3D

2G3N \| pdb_00002g3n	Download File View File

Crystal structure of the Sulfolobus solfataricus alpha-glucosidase MalA in complex with beta-octyl-glucopyranoside

Ernst, H.A., Lo Leggio, L., Willemoes, M., Leonard, G., Blum, P., Larsen, S.

(2006) J Mol Biology 358: 1106-1124

Released	2006-05-02
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	BOG

Explore in 3D

2HXB \| pdb_00002hxb	Download File View File

dCTP deaminase-dUTPase from Methanocaldococcus jannaschii

Bynck, J.H., Johansson, E.

To be published

Released	2007-08-14
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	dCTP deaminase, dUMP-forming (protein)

Explore in 3D

2HXD \| pdb_00002hxd	Download File View File

Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium

Bynck, J.H., Johansson, E.

To be published

Released	2007-08-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	dCTP deaminase, dUMP-forming (protein)
Unique Ligands	DUP, MG

Explore in 3D

2J4H \| pdb_00002j4h	Download File View File

Crystal structure of a H121A Escherichia coli dCTP deaminase mutant enzyme

Johansson, E., Thymark, M., Bynck, J.H., Fanoe, M., Larsen, S., Willemoes, M.

(2007) FEBS J 274: 4188

Released	2007-08-07
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli
Macromolecule	DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (protein)
Unique Ligands	MG, YYY

Explore in 3D

2J4Q \| pdb_00002j4q	Download File View File

Crystal structure of a E138A Escherichia coli dCTP deaminase mutant enzyme in complex with dTTP

Johansson, E., Thymark, M., Bynck, J.H., Fanoe, M., Larsen, S., Willemoes, M.

(2007) FEBS J 274: 4188

Released	2007-08-07
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli
Macromolecule	DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (protein)
Unique Ligands	MG, TTP, TYD

Explore in 3D

2QLP \| pdb_00002qlp	Download File View File

Bifunctional dCTP deaminase:dUTPase from Mycobacterium tuberculosis, apo form

Christophersen, S., Harris, P., Willemoes, M.

(2007) J Mol Biology 376: 554-569

Released	2008-02-19
Method	X-RAY DIFFRACTION 2.47 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Deoxycytidine triphosphate deaminase (protein)
Unique Ligands	1PE

Explore in 3D

2QPS \| pdb_00002qps	Download File View File

"Sugar tongs" mutant Y380A in complex with acarbose

Aghajari, N., Jensen, M.H., Tranier, S., Haser, R.

(2007) FEBS J 274: 5055-5067

Released	2008-02-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hordeum vulgare
Macromolecule	Alpha-amylase type A isozyme (protein)
Unique Ligands	CA

Explore in 3D

2QPU \| pdb_00002qpu	Download File View File

Sugar tongs mutant S378P in complex with acarbose

Aghajari, N., Jensen, M.H., Tranier, S., Haser, R.

(2007) FEBS J 274: 5055-5067

Released	2008-07-01
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Hordeum vulgare
Macromolecule	Alpha-amylase type A isozyme (protein)
Unique Ligands	BGC, CA, EDO, QPU
Unique branched monosaccharides	AC1, BGC, GLC

Explore in 3D

2QXX \| pdb_00002qxx	Download File View File

Bifunctional dCTP deaminase: dUTPase from Mycobacterium tuberculosis in complex with dTTP

Christophersen, S., Harris, P., Willemoes, M.

(2008) J Mol Biology 376: 554-569

Released	2008-02-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Deoxycytidine triphosphate deaminase (protein)
Unique Ligands	1PE, MG, TTP

Explore in 3D

2V9X \| pdb_00002v9x	Download File View File

E138D variant of Escherichia coli dCTP deaminase in complex with dUTP

Thymark, M., Johansson, E., Larsen, S., Willemoes, M.

(2008) Arch Biochem Biophys 470: 20

Released	2007-11-20
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (protein)
Unique Ligands	DUT, MG, SO4

Explore in 3D

3G6W \| pdb_00003g6w	Download File View File

Asymetric GTP bound structure of UPRTase from Sulfolobus solfataricus containing PRPP-mg2+ in half of the active sites and R5P and PPi in the other half

Kadziola, A., Christoffersen, S.

(2009) J Mol Biology 393: 464-477

Released	2009-09-01
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Uracil phosphoribosyltransferase (protein)
Unique Ligands	GTP, HSX, MG, POP, PRP

Explore in 3D

3GF0 \| pdb_00003gf0	Download File View File

Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145Q from Methanocaldococcus jannaschii in complex with pyrophosphate and magnesium

Siggaard, J.H.B., Johansson, E., Vognsen, T., Helt, S.S., Harris, P., Willemoes, M.

To be published

Released	2009-03-10
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	dCTP deaminase, dUMP-forming (protein)
Unique Ligands	MG, POP

Explore in 3D

3NVA \| pdb_00003nva	Download File View File

Dimeric form of CTP synthase from Sulfolobus solfataricus

Harris, P., Willemoes, M., Lauritsen, I., Johansson, E., Jensen, K.F.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 201-208

Released	2010-09-08
Method	X-RAY DIFFRACTION 2.504 Å
Organisms	Saccharolobus solfataricus
Macromolecule	CTP synthase (protein)

Explore in 3D

4A6A \| pdb_00004a6a	Download File View File

A115V variant of dCTP deaminase-dUTPase from Mycobacterium tuberculosis in complex with dTTP

Lovgreen, M.N., Ucar, E., Willemoes, M., Harris, P.

To be published

Released	2012-10-10
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (protein)
Unique Ligands	MG, TTP

Explore in 3D

4XJC \| pdb_00004xjc	Download File View File

dCTP deaminase-dUTPase from Bacillus halodurans

Oehlenschlaeger, C., Loevgreen, M., Willemoes, M., Harris, P.

(2015) Appl Environ Microbiol 81: 3395-3404

Released	2015-03-18
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Halalkalibacterium halodurans C-125
Macromolecule	Deoxycytidine triphosphate deaminase (protein)
Unique Ligands	MG, PEG, TTP

Explore in 3D

5J7D \| pdb_00005j7d	Download File View File

Computationally Designed Thioredoxin dF106

Horowitz, S., Johansen, N., Olsen, J.G., Winther, J.R.

(2016) J Mol Biology 428: 4361-4377

Released	2016-10-05
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	synthetic construct
Macromolecule	Designed Thioredoxin dF106 (protein)
Unique Ligands	CU

Explore in 3D

8QYE \| pdb_00008qye	Download File View File

Catalytic core of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF) concieved by deep network hallucination: dEngBF4

Aghajari, N.

(2024) ACS Synth Biol 13: 862-875

Released	2024-03-06
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	synthetic construct
Macromolecule	ENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE (protein)
Unique Ligands	EDO

1 to 25 of 26 Structures

Page 1 of 2

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1UWZ | pdb_00001uwz

1UX0 | pdb_00001ux0

1UX1 | pdb_00001ux1

1VST | pdb_00001vst

1XS1 | pdb_00001xs1

1XS4 | pdb_00001xs4

1XS6 | pdb_00001xs6

2G3M | pdb_00002g3m

2G3N | pdb_00002g3n

2HXB | pdb_00002hxb

2HXD | pdb_00002hxd

2J4H | pdb_00002j4h

2J4Q | pdb_00002j4q

2QLP | pdb_00002qlp

2QPS | pdb_00002qps

2QPU | pdb_00002qpu

2QXX | pdb_00002qxx

2V9X | pdb_00002v9x

3G6W | pdb_00003g6w

3GF0 | pdb_00003gf0

3NVA | pdb_00003nva

4A6A | pdb_00004a6a

4XJC | pdb_00004xjc

5J7D | pdb_00005j7d

8QYE | pdb_00008qye