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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Wojdyla, J.A."

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Search Summary

This query matches 125 Structures.

Refinements

Structure Determination Methodology

experimental (125)

Scientific Name of Source Organism

	Cryphonectria parasitica (55)
	Homo sapiens (30)
	Mycobacterium tuberculosis H37Rv (7)
	Escherichia coli (5)
	Feline infectious peritonitis virus (strain 79-1146) (3)
	Human coronavirus HKU1 (isolate N1) (2)
	Klebsiella pneumoniae (2)
	Mus musculus (2)
	Mycobacterium tuberculosis H37Ra (2)
	Pseudomonas aeruginosa (2)

More...

Taxonomy

	Eukaryota (89)
	Bacteria (22)
	Riboviria (13)
	unclassified sequences (1)

Experimental Method

X-RAY DIFFRACTION (125)

Polymer Entity Type

Protein (125)

Refinement Resolution (Å)

	1.0 - 1.5 (23)
	1.5 - 2.0 (70)
	2.0 - 2.5 (18)
	2.5 - 3.0 (8)
	3.0 - 3.5 (5)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (7)
	2015 - 2019 (14)
	2020 - 2024 (101)

Enzyme Classification Name

	Hydrolases (65)
	Translocases (4)
	Ligases (2)
	Transferases (1)

Membrane Protein Annotation

	MemProtMD (1)
	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (122)
	Cyclic (5)

SCOP Classification

	Artifacts (35)
	All beta proteins (30)
	Alpha and beta proteins (a+b) (6)
	All alpha proteins (5)
	Alpha and beta proteins (a/b) (3)

AllSelected

1 to 25 of 125 Structures

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3ETI \| pdb_00003eti	Download File View File

Structure of a cubic crystal form of X (ADRP) domain from FCoV

Wojdyla, J.A., Manolaridis, I., Tucker, P.A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1292-1300

Released	2009-10-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Feline infectious peritonitis virus (strain 79-1146)
Macromolecule	macro domain of Non-structural protein 3 (protein)

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3EW5 \| pdb_00003ew5	Download File View File

Structure of the tetragonal crystal form of X (ADRP) domain from FCoV

Wojdyla, J.A., Manolaridis, I., Tucker, P.A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1292-1300

Released	2009-10-27
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Feline infectious peritonitis virus (strain 79-1146)
Macromolecule	macro domain of Non-structural protein 3 (protein)
Unique Ligands	1GP, CL, SO4

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3GZF \| pdb_00003gzf	Download File View File

Structure of the C-terminal domain of nsp4 from Feline Coronavirus

Manolaridis, I., Wojdyla, J.A., Panjikar, S., Snijder, E.J., Gorbalenya, A.E., Coutard, B., Tucker, P.A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 839-846

Released	2009-08-18
Method	X-RAY DIFFRACTION 2.756 Å
Organisms	Feline coronavirus
Macromolecule	Replicase polyprotein 1ab (protein)
Unique Ligands	SO4

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3JZT \| pdb_00003jzt	Download File View File

Structure of a cubic crystal form of X (ADRP) domain from FCoV with ADP-ribose

Wojdyla, J.A., Manolaridis, I., Tucker, P.A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1292-1300

Released	2010-01-12
Method	X-RAY DIFFRACTION 3.91 Å
Organisms	Feline infectious peritonitis virus (strain 79-1146)
Macromolecule	macro domain of Non-structural protein 3 (protein)
Unique Ligands	APR, CL, NA

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3MP2 \| pdb_00003mp2	Download File View File

Crystal structure of transmissible gastroenteritis virus papain-like protease 1

Wojdyla, J.A., Manolaridis, I., Tucker, P.A.

(2010) J Virol 84: 10063-10073

Released	2010-09-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Porcine transmissible gastroenteritis coronavirus strain Purdue
Macromolecule	Non-structural protein 3 (protein)
Unique Ligands	ZN

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3O0E \| pdb_00003o0e	Download File View File

Crystal structure of OmpF in complex with colicin peptide OBS1

Wojdyla, J.A., Housden, N.G., Korczynska, J., Grishkovskaya, I., Kirkpatrick, N., Brzozowski, A.M., Kleanthous, C.

(2010) Proc Natl Acad Sci U S A 107: 21412-21417

Released	2010-12-08
Method	X-RAY DIFFRACTION 3.01 Å
Organisms	Escherichia coli
Macromolecule	Colicin-E9 (protein) Porin OmpF (protein)
Unique Ligands	BOG

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3TIP \| pdb_00003tip	Download File View File

Crystal structure of Staphylococcus aureus SasG E-G52 module

Gruszka, D.T., Wojdyla, J.A., Turkenburg, J.P., Potts, J.R.

(2012) Proc Natl Acad Sci U S A 109: E1011-E1018

Released	2012-04-18
Method	X-RAY DIFFRACTION 1.7009 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325
Macromolecule	Surface protein G (protein)

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3TIQ \| pdb_00003tiq	Download File View File

Crystal structure of Staphylococcus aureus SasG G51-E-G52 module

Gruszka, D.T., Wojdyla, J.A., Turkenburg, J.P., Potts, J.R.

(2012) Proc Natl Acad Sci U S A 109: E1011-E1018

Released	2012-04-18
Method	X-RAY DIFFRACTION 1.8739 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325
Macromolecule	Surface protein G (protein)
Unique Ligands	MG, TRS

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3U43 \| pdb_00003u43	Download File View File

Crystal structure of the colicin E2 DNase-Im2 complex

Wojdyla, J.A., Kleanthous, C.

(2012) J Mol Biology 417: 79-94

Released	2012-03-21
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Escherichia coli
Macromolecule	Colicin-E2 (protein) Colicin-E2 immunity protein (protein)
Unique Ligands	CA, ZN

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4JML \| pdb_00004jml	Download File View File

Crystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) complex.

Wojdyla, J.A., Klein, A., Kleanthous, C.

(2013) Science 340: 1570-1574

Released	2013-07-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli Escherichia coli DH1
Macromolecule	Colicin-E9 (protein) Protein TolB (protein)
Unique Ligands	CA

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4QAY \| pdb_00004qay	Download File View File

Crystal structure of TamA POTRA domains

Wojdyla, J.A., Mosbahi, K., Walker, D., Kleanthous, C.

To be published

Released	2015-11-18
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	human gut metagenome
Macromolecule	Translocation and assembly module TamA (protein)
Unique Ligands	PO4

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4UHP \| pdb_00004uhp	Download File View File

Crystal structure of the pyocin AP41 DNase-Immunity complex

Joshi, A., Chen, S., Wojdyla, J.A., Kaminska, R., Kleanthous, C.

(2015) J Mol Biology 427: 2852

Released	2015-08-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	BACTERIOCIN IMMUNITY PROTEIN (protein) LARGE COMPONENT OF PYOCIN AP41 (protein)

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4UHQ \| pdb_00004uhq	Download File View File

Crystal structure of the pyocin AP41 DNase

Joshi, A., Chen, S., Wojdyla, J.A., Kaminska, R., Kleanthous, C.

(2015) J Mol Biology 427: 2852

Released	2015-08-05
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	LARGE COMPONENT OF PYOCIN AP41 (protein)
Unique Ligands	CIT, NI

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5BY4 \| pdb_00005by4	Download File View File

Structure and function of the Escherichia coli Tol-Pal stator protein TolR

Wojdyla, J.A., Kaminska, R., Kleanthous, C.

(2015) J Biological Chem 290: 26675-26687

Released	2015-09-16
Method	X-RAY DIFFRACTION 1.702 Å
Organisms	Escherichia coli
Macromolecule	Protein TolR (protein)
Unique Ligands	NA

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5EW5 \| pdb_00005ew5	Download File View File

Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9

Klein, A., Wojdyla, J.A., Kleanthous, C.

(2016) Biochem J 473: 2799-2812

Released	2016-07-20
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Escherichia coli
Macromolecule	Colicin-E9 (protein) Colicin-E9 immunity protein (protein)

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5GNB \| pdb_00005gnb	Download File View File

Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 2.3 angstrom, native-SAD phasing)

Guan, H., Wojdyla, J.A., Wang, M., Cui, S.

(2017) Nat Commun 8: 15216-15216

Released	2017-06-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Human coronavirus HKU1 (isolate N1)
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG

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5KWB \| pdb_00005kwb	Download File View File

Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 1.9 angstrom, molecular replacement)

Guan, H., Wojdyla, J.A., Wang, M., Cui, S.

(2017) Nat Commun 8: 15216-15216

Released	2017-06-07
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Human coronavirus HKU1 (isolate N1)
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	MG, NAG
Unique branched monosaccharides	FRU, GLC

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5WWP \| pdb_00005wwp	Download File View File

Crystal structure of Middle East respiratory syndrome coronavirus helicase (MERS-CoV nsp13)

Hao, W., Wojdyla, J.A., Zhao, R., Han, R., Das, R., Zlatev, I., Manoharan, M., Wang, M., Cui, S.

(2017) PLoS Pathog 13: e1006474-e1006474

Released	2017-07-05
Method	X-RAY DIFFRACTION 3 Å
Organisms	Human betacoronavirus 2c EMC/2012
Macromolecule	ORF1ab (protein)
Unique Ligands	SO4, ZN

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5XET \| pdb_00005xet	Download File View File

Crystal structure of Mycobacterium tuberculosis methionyl-tRNA synthetase bound by methionyl-adenylate (Met-AMP)

Wang, W., Qin, B., Wojdyla, J.A., Wang, M., Gao, X., Cui, S.

(2018) IUCrJ 5: 478-490

Released	2018-07-11
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	Mycobacterium tuberculosis H37Ra
Macromolecule	Methionine--tRNA ligase (protein)
Unique Ligands	EDO, ME8, MG

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5XGQ \| pdb_00005xgq	Download File View File

Crystal structure of apo form (free-state) Mycobacterium tuberculosis methionyl-tRNA synthetase

Wang, W., Wang, M., Wojdyla, J.A., Cui, S.

(2018) IUCrJ 5: 478-490

Released	2018-07-11
Method	X-RAY DIFFRACTION 1.899 Å
Organisms	Mycobacterium tuberculosis H37Ra
Macromolecule	Methionine-tRNA ligase (protein)

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5ZO1 \| pdb_00005zo1	Download File View File

Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ectodomain (Ig1-Ig3), 2.2A

Liu, X., An, T., Li, D., Fan, Z., Xiang, P., Li, C., Ju, W., Li, J., Hu, G., Qin, B., Yin, B., Wojdyla, J.A., Wang, M., Yuan, J., Qiang, B., Shu, P., Cui, S., Peng, X.

(2019) Proc Natl Acad Sci U S A 116: 2068-2077

Released	2019-01-30
Method	X-RAY DIFFRACTION 2.201 Å
Organisms	Mus musculus
Macromolecule	Cell adhesion molecule 4 (protein)
Unique Ligands	GOL
Unique branched monosaccharides	FUC, NAG

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5ZO2 \| pdb_00005zo2	Download File View File

Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ectodomain in complex with mouse nectin-like molecule 1 (mNecl-1) Ig1 domain, 3.3A

Liu, X., An, T., Li, D., Fan, Z., Xiang, P., Li, C., Ju, W., Li, J., Hu, G., Qin, B., Yin, B., Wojdyla, J.A., Wang, M., Yuan, J., Qiang, B., Shu, P., Cui, S., Peng, X.

(2019) Proc Natl Acad Sci U S A 116: 2068-2077

Released	2019-01-30
Method	X-RAY DIFFRACTION 3.29 Å
Organisms	Mus musculus
Macromolecule	Cell adhesion molecule 3 (protein) Cell adhesion molecule 4 (protein)
Unique branched monosaccharides	FUC, NAG

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6I59 \| pdb_00006i59	Download File View File

Long wavelength native-SAD phasing of Sen1 helicase

Basu, S., Olieric, V., Matsugaki, N., Kawano, Y., Takashi, T., Huang, C.Y., Leonarski, F., Yamada, Y., Vera, L., Olieric, N., Basquin, J., Wojdyla, J.A., Diederichs, K., Yamamoto, M., Bunk, O., Wang, M.

(2019) IUCrJ 6: 373-386

Released	2019-03-13
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Helicase SEN1 (protein)
Unique Ligands	ADP, EDO, GOL, MG, PEG

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6I5C \| pdb_00006i5c	Download File View File

Long wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex

(2019) IUCrJ 6: 373-386

Released	2019-03-13
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Bos taurus Gallus gallus Rattus norvegicus
Macromolecule	Stathmin-4 (protein) TUBULIN-TYROSINE LIGASE (protein) Tubulin alpha-1B chain (protein) Tubulin beta-2B chain (protein)
Unique Ligands	ACP, CA, CL, GDP, GTP, MES, MG

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6J7N \| pdb_00006j7n	Download File View File

Crystal structure of toxin TglT (unusual type guanylyltransferase-like toxin, Rv1045) mutant D82A co-expressed with TakA from Mycobacterium tuberculosis

Yu, X., Gao, X., Zhu, K., Wojdyla, J.A., Wang, M., Cui, S.

(2020) Commun Biol 3: 216-216

Released	2020-05-13
Method	X-RAY DIFFRACTION 2.294 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	guanylyltransferase-like toxin (protein)
Unique Ligands	MG

1 to 25 of 125 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

3ETI | pdb_00003eti

3EW5 | pdb_00003ew5

3GZF | pdb_00003gzf

3JZT | pdb_00003jzt

3MP2 | pdb_00003mp2

3O0E | pdb_00003o0e

3TIP | pdb_00003tip

3TIQ | pdb_00003tiq

3U43 | pdb_00003u43

4JML | pdb_00004jml

4QAY | pdb_00004qay

4UHP | pdb_00004uhp

4UHQ | pdb_00004uhq

5BY4 | pdb_00005by4

5EW5 | pdb_00005ew5

5GNB | pdb_00005gnb

5KWB | pdb_00005kwb

5WWP | pdb_00005wwp

5XET | pdb_00005xet

5XGQ | pdb_00005xgq

5ZO1 | pdb_00005zo1

5ZO2 | pdb_00005zo2

6I59 | pdb_00006i59

6I5C | pdb_00006i5c

6J7N | pdb_00006j7n