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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Knighton, D.R."

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Search Summary

This query matches 50 Structures.

Refinements

Structure Determination Methodology

experimental (50)

Scientific Name of Source Organism

	Staphylococcus aureus (12)
	Homo sapiens (10)
	Streptococcus pyogenes (6)
	Streptococcus pyogenes serotype M1 (6)
	synthetic construct (4)
	Panax quinquefolius (3)
	Streptococcus thermophilus (3)
	Streptococcus thermophilus LMD-9 (3)
	Danio rerio (2)
	Escherichia coli K-12 (2)

More...

Taxonomy

	Bacteria (34)
	Eukaryota (17)
	other sequences (4)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (47)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

	Protein (46)
	DNA (17)
	RNA (12)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (10)
	2.0 - 2.5 (12)
	2.5 - 3.0 (12)
	3.0 - 3.5 (9)
	3.5 - 4.0 (2)

Release Date

	2010 - 2014 (8)
	2015 - 2019 (21)
	2020 - 2024 (18)
	2025 - 2029 (3)

Enzyme Classification Name

	Hydrolases (15)
	Transferases (5)
	Oxidoreductases (3)

Symmetry Type

	Asymmetric (31)
	Cyclic (8)
	Dihedral (8)

SCOP Classification

	All beta proteins (1)
	All alpha proteins (4)
	Alpha and beta proteins (a/b) (5)
	Artifacts (2)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 25 of 50 Structures

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3T8R \| pdb_00003t8r	Download File View File

Crystal structure of Staphylococcus aureus CymR

He, C., Ji, Q.

(2012) J Biological Chem 287: 21102-21109

Released	2012-05-16
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Staphylococcus aureus subsp. aureus Mu50
Macromolecule	Staphylococcus aureus CymR (protein)

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3T8T \| pdb_00003t8t	Download File View File

Crystal structure of Staphylococcus aureus CymR oxidized form

He, C., Ji, Q.

(2012) J Biological Chem 287: 21102-21109

Released	2012-05-16
Method	X-RAY DIFFRACTION 1.752 Å
Organisms	Staphylococcus aureus subsp. aureus Mu50
Macromolecule	Staphylococcus aureus CymR (oxidized form) (protein)

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4GXO \| pdb_00004gxo	Download File View File

Crystal structure of Staphylococcus aureus protein SarZ mutant C13E

Sun, F., Ding, Y., Ji, Q., Liang, Z., Deng, X., Wong, C.C., Yi, C., Zhang, L., Xie, S., Alvarez, S., Hicks, L.M., Luo, C., Jiang, H., Lan, L., He, C.

(2012) Proc Natl Acad Sci U S A 109: 15461-15466

Released	2012-09-26
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Staphylococcus aureus subsp. aureus str. Newman
Macromolecule	MarR family regulatory protein (protein)
Unique Ligands	GOL

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4HQE \| pdb_00004hqe	Download File View File

The crystal structure of QsrR-DNA complex

He, C., Ji, Q., Zhang, L.

(2013) Proc Natl Acad Sci U S A 110: 5010-5015

Released	2013-03-06
Method	X-RAY DIFFRACTION 2.299 Å
Organisms	Staphylococcus aureus synthetic construct
Macromolecule	Transcriptional regulator QsrR (protein) DNA (5'-D(APGPTPAPTPAPAPTPTPAPTPTPAPTPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPAPTPAPAPTPAPAPTPTPAPTPAPCPT)-3') (nucleic acid)

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4HQM \| pdb_00004hqm	Download File View File

The crystal structure of QsrR-menadione complex

Ji, Q., Zhang, L., Jones, M.B., Sun, F., Deng, X., Liang, H., Brugarolas, P., Gao, N., Peterson, S.N., Lan, L., Bae, T., He, C.

(2013) Proc Natl Acad Sci U S A 110: 5010-5015

Released	2013-03-06
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Staphylococcus aureus
Macromolecule	QsrR protein (protein)
Unique Ligands	17Z

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4ID7 \| pdb_00004id7	Download File View File

ACK1 kinase in complex with the inhibitor cis-3-[8-amino-1-(4-phenoxyphenyl)imidazo[1,5-a]pyrazin-3-yl]cyclobutanol

Jin, M., Wang, J., Kleinberg, A., Kadalbajoo, M., Siu, K., Cooke, A., Bittner, M., Yao, Y., Thelemann, A., Ji, Q., Bhagwat, S., Crew, A.P., Pachter, J., Epstein, D., Mulvihill, M.J.

(2013) Bioorg Med Chem Lett 23: 979-984

Released	2013-01-30
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Activated CDC42 kinase 1 (protein)
Unique Ligands	1G0, SO4

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4NPL \| pdb_00004npl	Download File View File

Crystal structure of Zebrafish ALKBH5 in complex with alpha-ketoglutarate

He, C., Chen, W., Zhang, L.

(2014) FEBS Lett 588: 892-898

Released	2014-02-19
Method	X-RAY DIFFRACTION 1.651 Å
Organisms	Danio rerio
Macromolecule	RNA demethylase ALKBH5 (protein)
Unique Ligands	AKG, MN

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4NPM \| pdb_00004npm	Download File View File

Crystal structure of Zebrafish ALKBH5 in complex with succinic acid

He, C., Chen, W., Zhang, L.

(2014) FEBS Lett 588: 892-898

Released	2014-02-19
Method	X-RAY DIFFRACTION 1.803 Å
Organisms	Danio rerio
Macromolecule	RNA demethylase ALKBH5 (protein)
Unique Ligands	MN, SIN

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4YWZ \| pdb_00004ywz	Download File View File

Crystal structure of the extracellular receptor domain of the essential sensor kinase WalK from Staphylococcus aureus

Ji, Q., Wawrzak, Z., He, C.

(2016) Nat Commun 7: 11000-11000

Released	2016-03-30
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Staphylococcus aureus
Macromolecule	Sensor protein kinase WalK (protein)

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5C0Z \| pdb_00005c0z	Download File View File

The structure of oxidized rat cytochrome c at 1.13 angstroms resolution

Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.

(2019) FASEB J fj201901120R-fj201901120R

Released	2016-09-21
Method	X-RAY DIFFRACTION 1.1236 Å
Organisms	Rattus norvegicus
Macromolecule	Cytochrome c, somatic (protein)
Unique Ligands	FC6, HEC

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5EPO \| pdb_00005epo	Download File View File

The three-dimensional structure of Clostridium absonum 7alpha-hydroxysteroid dehydrogenase

Lou, D., Wang, B., Wang, F.

(2016) Sci Rep 6: 22885-22885

Released	2016-03-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Clostridium sardiniense
Macromolecule	7-alpha-hydroxysteroid deydrogenase (protein)
Unique Ligands	GOL, NAP, TUD

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5XS9 \| pdb_00005xs9	Download File View File

Crystal structure of Mycobacterium smegmatis BioQ

Zhang, Y., Ji, Q., Feng, Y.

To be published

Released	2018-06-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	TetR family transcriptional regulator (protein)

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5Y6I \| pdb_00005y6i	Download File View File

Crystal structure of Pseudomonas aeruginosa HmgR

Gu, T., Ji, Q., Liang, H.

To be published

Released	2018-08-15
Method	X-RAY DIFFRACTION 2.517 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Transcriptional regulator KdgR (protein)

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5YH5 \| pdb_00005yh5	Download File View File

The crystal structure of Staphylococcus aureus CntA in apo form

Song, L., Ji, Q.

(2018) Proc Natl Acad Sci U S A 115: 3942-3947

Released	2018-03-28
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Staphylococcus aureus
Macromolecule	Nickel ABC transporter substrate-binding protein (protein)
Unique Ligands	EDO, PEG

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5YH8 \| pdb_00005yh8	Download File View File

The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and nickel

Ji, Q., Song, L.

(2018) Proc Natl Acad Sci U S A 115: 3942-3947

Released	2018-03-28
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Staphylococcus aureus
Macromolecule	Nickel ABC transporter substrate-binding protein (protein)
Unique Ligands	8UX, GOL, NI, PEG

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5YHE \| pdb_00005yhe	Download File View File

The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and cobalt

Song, L., Ji, Q.

(2018) Proc Natl Acad Sci U S A 115: 3942-3947

Released	2018-03-28
Method	X-RAY DIFFRACTION 2.465 Å
Organisms	Staphylococcus aureus
Macromolecule	Nickel ABC transporter substrate-binding protein (protein)
Unique Ligands	8UX, ACT, CL, CO

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5YHG \| pdb_00005yhg	Download File View File

The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and zinc

Ji, Q., Song, L.

(2018) Proc Natl Acad Sci U S A 115: 3942-3947

Released	2018-03-28
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Staphylococcus aureus
Macromolecule	Nickel ABC transporter substrate-binding protein (protein)
Unique Ligands	8UX, ACT, CL, GOL, PEG, ZN

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5ZAS \| pdb_00005zas	Download File View File

Crystal structure of 5-formylcytosine containing decamer dsDNA

Fu, T.R., Zhang, L.

(2019) Chem Sci 10: 7407-7417

Released	2019-02-13
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(5FC)PGPCPTPGPG)-3') (nucleic acid)
Unique Ligands	BCT

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5ZAT \| pdb_00005zat	Download File View File

Crystal structure of 5-carboxylcytosine containing decamer dsDNA

Fu, T.R., Zhang, L.

(2019) Chem Sci 10: 7407-7417

Released	2019-02-13
Method	X-RAY DIFFRACTION 1.06 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(CAC)PGPCPTPGPG)-3') (nucleic acid)

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6IKM \| pdb_00006ikm	Download File View File

Crystal structure of SpuE-Spermidine in complex with ScFv5

Wu, D., Sun, X.

(2019) J Mol Biology 431: 4882-4896

Released	2019-12-25
Method	X-RAY DIFFRACTION 3.398 Å
Organisms	Homo sapiens Pseudomonas aeruginosa
Macromolecule	Polyamine transport protein (protein) ScFv5 (protein)
Unique Ligands	SO4, SPD

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6JV3 \| pdb_00006jv3	Download File View File

Crystal structure of 5-hydoxylmethylcytosine containing decamer dsDNA

Zhang, L., Wang, Y.X.

(2019) Chem Sci 10: 7407-7417

Released	2019-07-31
Method	X-RAY DIFFRACTION 2.851 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(5HC)PGPCPTPGPG)-3') (nucleic acid)

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6JV5 \| pdb_00006jv5	Download File View File

Crystal structure of 5-methylcytosine containing decamer dsDNA

Zhang, L., Wang, Y.X.

(2019) Chem Sci 10: 7407-7417

Released	2019-07-31
Method	X-RAY DIFFRACTION 1.401 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(5CM)PGPCPTPGPG)-3') (nucleic acid)

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6K3Z \| pdb_00006k3z	Download File View File

Crystal structure of dCas9 in complex with sgRNA and DNA (TGA PAM)

Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J., Ji, Q.

(2019) PLoS Biol 17: e3000496-e3000496

Released	2019-09-25
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Streptococcus pyogenes Streptococcus pyogenes serotype M1
Macromolecule	CRISPR-associated endonuclease Cas9 (protein) DNA (28-MER) (nucleic acid) DNA (5'-D(APAPAPTPGPAPTPAPTPTP*G)-3') (nucleic acid) RNA (81-MER) (nucleic acid)

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6K4P \| pdb_00006k4p	Download File View File

Crystal structure of xCas9 in complex with sgRNA and DNA (TGG PAM)

Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J., Ji, Q.

(2019) PLoS Biol 17: e3000496-e3000496

Released	2019-09-25
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Streptococcus pyogenes Streptococcus pyogenes serotype M1
Macromolecule	CRISPR-associated endonuclease Cas9/Csn1 (protein) DNA (28-MER) (nucleic acid) non-targeted DNA (nucleic acid) sgRNA (nucleic acid)
Unique Ligands	PO4

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6K4Q \| pdb_00006k4q	Download File View File

Crystal structure of xCas9 in complex with sgRNA and DNA (CGG PAM)

Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J., Ji, Q.

(2019) PLoS Biol 17: e3000496-e3000496

Released	2019-09-25
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Streptococcus pyogenes Streptococcus pyogenes serotype M1
Macromolecule	CRISPR-associated endonuclease Cas9/Csn1 (protein) DNA (28-MER) (nucleic acid) DNA (5'-D(APAPAPCPGPGPTPAPTPTP*G)-3') (nucleic acid) sgRNA (nucleic acid)
Unique Ligands	PO4

1 to 25 of 50 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

Symmetry Type

SCOP Classification

3T8R | pdb_00003t8r

3T8T | pdb_00003t8t

4GXO | pdb_00004gxo

4HQE | pdb_00004hqe

4HQM | pdb_00004hqm

4ID7 | pdb_00004id7

4NPL | pdb_00004npl

4NPM | pdb_00004npm

4YWZ | pdb_00004ywz

5C0Z | pdb_00005c0z

5EPO | pdb_00005epo

5XS9 | pdb_00005xs9

5Y6I | pdb_00005y6i

5YH5 | pdb_00005yh5

5YH8 | pdb_00005yh8

5YHE | pdb_00005yhe

5YHG | pdb_00005yhg

5ZAS | pdb_00005zas

5ZAT | pdb_00005zat

6IKM | pdb_00006ikm

6JV3 | pdb_00006jv3

6JV5 | pdb_00006jv5

6K3Z | pdb_00006k3z

6K4P | pdb_00006k4p

6K4Q | pdb_00006k4q