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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Khalil, A."

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Search Summary

This query matches 33 Structures.

Refinements

Structure Determination Methodology

experimental (33)

Scientific Name of Source Organism

	Mycobacterium tuberculosis H37Rv (10)
	Pseudomonas aeruginosa UCBPP-PA14 (4)
	Mycolicibacterium smegmatis (3)
	Pseudomonas aeruginosa (3)
	Thermotoga maritima MSB8 (3)
	Mycobacterium tuberculosis CDC1551 (2)
	Streptomyces clavuligerus (2)
	Homo sapiens (1)
	Plasmodium falciparum 3D7 (1)
	Streptomyces yokosukanensis (1)

More...

Taxonomy

	Bacteria (30)
	Eukaryota (2)

Experimental Method

	X-RAY DIFFRACTION (32)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (32)
	DNA (1)

Refinement Resolution (Å)

	1.5 - 2.0 (9)
	2.0 - 2.5 (13)
	2.5 - 3.0 (9)
	3.0 - 3.5 (1)

Release Date

	1995 - 1999 (1)
	2015 - 2019 (21)
	2020 - 2024 (11)

Enzyme Classification Name

	Transferases (21)
	Oxidoreductases (3)

Symmetry Type

	Cyclic (14)
	Asymmetric (9)
	Dihedral (9)

SCOP Classification

	Alpha and beta proteins (a/b) (9)
	All beta proteins (1)
	Artifacts (4)

AllSelected

1 to 25 of 33 Structures

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1PIK	Download File View File

ESPERAMICIN A1-DNA COMPLEX, NMR, 4 STRUCTURES

Kumar, R.A., Ikemoto, N., Patel, D.J.

(1997) J Mol Biology 265: 173-186

Released	1997-03-12
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CGPGPAPTPCPCP*GP)-3') (nucleic acid)
Unique Ligands	DLF, DPA, MTC, TMR
Unique branched monosaccharides	DAG, MAT

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5GM8	Download File View File

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa

Jaroensuk, J., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Liew, C.W., McBee, M.E., Thongdee, N., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M.

(2016) Nucleic Acids Res 44: 10834-10848

Released	2016-10-26
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ (protein)
Unique Ligands	SFG

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5GMB	Download File View File

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa

Jaroensuk, J., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Liew, C.W., McBee, M.E., Thongdee, N., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M.

(2016) Nucleic Acids Res 44: 10834-10848

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ (protein)

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5GMC	Download File View File

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa

Jaroensuk, J., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Liew, C.W., McBee, M.E., Thongdee, N., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M.

(2016) Nucleic Acids Res 44: 10834-10848

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ (protein)

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5WRP	Download File View File

T-state crystal structure of pyruvate kinase from Mycobacterium tuberculosis

Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

(2017) Nat Commun 8: 1986-1986

Released	2017-11-15
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	PO4

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5WS8	Download File View File

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate

Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

(2017) Nat Commun 8: 1986-1986

Released	2017-11-15
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	MG, OXL

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5WS9	Download File View File

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, ATP and allosteric activator AMP

Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

(2017) Nat Commun 8: 1986-1986

Released	2017-11-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	AMP, ATP, K, MG, OXL, PO4

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5WSA	Download File View File

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate and allosteric activator Glucose 6-Phosphate

Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

(2017) Nat Commun 8: 1986-1986

Released	2017-11-15
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	G6P, MG, OXL, PO4

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5WSB	Download File View File

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, allosteric activators AMP and Glucose 6-Phosphate

Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

(2017) Nat Commun 8: 1986-1986

Released	2017-11-15
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	AMP, G6P, K, MG, OXL, PO4

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5WSC	Download File View File

Crystal of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, soaked with allosteric activators AMP and Glucose 6-Phosphate

Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

(2017) Nat Commun 8: 1986-1986

Released	2017-11-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	AMP, G6P, K, MG, OXL, PO4

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5XAJ	Download File View File

Structural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex.

Wong, Y.H., Goh, B.C., Lescar, J.

(2017) J Virol

Released	2017-06-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Fab E1 heavy chain (protein) Fab E1 light chain (protein) FabHM14c10 heavy chain (protein) FabHM14c10 light chain (protein)

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5ZHI	Download File View File

Apo crystal structure of TrmD from Mycobacterium tuberculosis

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-03-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)

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5ZHJ	Download File View File

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with S-adenosyl homocysteine (SAH)

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-03-06
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	GOL, SAH

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5ZHK	Download File View File

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-03-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	9D6

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5ZHL	Download File View File

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-03-06
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	9D0

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5ZHM	Download File View File

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-03-06
Method	X-RAY DIFFRACTION 2.76 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	9D3, SAM

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5ZHN	Download File View File

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-03-27
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	9D0

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6ITO	Download File View File

Crystal structure of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, AMP and inhibitor Ribose 5-Phosphate

Zhong, W., Cai, Q., El Sahili, A., Mu, Y., Lescar, J., Dedon, P.C.

(2019) J Mol Biology 431: 3690-3705

Released	2019-08-14
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	AMP, MG, OXL, R5P

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6JIV	Download File View File

SspE crystal structure

Bing, Y.Z., Yang, H.G.

(2020) Nat Microbiol 5: 917-928

Released	2020-03-25
Method	X-RAY DIFFRACTION 3.31 Å
Organisms	Streptomyces yokosukanensis
Macromolecule	SspE protein (protein)

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6JKI	Download File View File

Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa

Jaroensuk, J., Liew, C.W., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Zhong, W.H., McBee, M.E., Thongdee, N., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M.

(2019) RNA 25: 1481-1496

Released	2019-07-03
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	GOL, MN, NA, PEG, SFG

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6JOE	Download File View File

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-09-04
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Pseudomonas aeruginosa UCBPP-PA14
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	BWR, PO4, SAM

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6JOF	Download File View File

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

Released	2019-09-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	BWR

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6JUF	Download File View File

SspB crystal structure

Liqiong, L., Yubing, Z.

(2020) Nat Microbiol 5: 917-928

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.587 Å
Organisms	Streptomyces clavuligerus
Macromolecule	SspB protein (protein)

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6KSH	Download File View File

Crystal structure of pyruvate kinase (PYK) from Plasmodium falciparum in complex with oxalate and ATP

Zhong, W., Cai, Q., Li, K., Lescar, J., Dedon, P.C.

(2020) Biochem Biophys Res Commun 532: 370-376

Released	2020-08-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Pyruvate kinase (protein)
Unique Ligands	ATP, K, MG, OXL

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6LB9	Download File View File

Magnesium ion-bound SspB crystal structure

Liqiong, L., Yubing, Z.

(2020) Nat Microbiol 5: 917-928

Released	2020-03-25
Method	X-RAY DIFFRACTION 2.227 Å
Organisms	Streptomyces clavuligerus
Macromolecule	DUF4007 domain-containing protein (protein)
Unique Ligands	MG