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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Gao, R."

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Search Summary

This query matches 51 Structures.

Refinements

Structure Determination Methodology

experimental (51)

Scientific Name of Source Organism

	Homo sapiens (13)
	Mycolicibacterium smegmatis MC2 155 (8)
	Escherichia coli (6)
	Aeropyrum pernix (5)
	Human papillomavirus 16 (5)
	Caenorhabditis elegans (3)
	Human betaherpesvirus 5 (3)
	Micropechis ikaheca (3)
	Oryza sativa (3)
	Trichomonas vaginalis G3 (3)

More...

Taxonomy

	Eukaryota (29)
	Bacteria (17)
	Archaea (7)
	Monodnaviria (5)
	Duplodnaviria (4)
	other sequences (2)

Experimental Method

	X-RAY DIFFRACTION (29)
	ELECTRON MICROSCOPY (21)
	SOLID-STATE NMR (1)

Polymer Entity Type

	Protein (51)
	DNA (2)
	NA-hybrid (1)

Refinement Resolution (Å)

	1.5 - 2.0 (10)
	2.0 - 2.5 (10)
	2.5 - 3.0 (13)
	3.0 - 3.5 (7)
	3.5 - 4.0 (4)
	4.0 - 4.5 (5)
	> 4.5 (1)

Release Date

	2000 - 2004 (6)
	2005 - 2009 (5)
	2010 - 2014 (6)
	2015 - 2019 (2)
	2020 - 2024 (32)

Enzyme Classification Name

	Hydrolases (20)
	Transferases (12)
	Isomerases (3)
	Oxidoreductases (1)
	Translocases (1)

Membrane Protein Annotation

	PDBTM (15)
	OPM (12)
	mpstruc (8)
	MemProtMD (9)

Symmetry Type

	Asymmetric (19)
	Cyclic (30)
	Dihedral (2)
	Tetrahedral (1)

SCOP Classification

	All alpha proteins (8)
	All beta proteins (6)
	Alpha and beta proteins (a/b) (5)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 51 Structures

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1KU5 \| pdb_00001ku5	Download File View File

Crystal Structure of recombinant histone HPhA from hyperthermophilic archaeon Pyrococcus horikoshii OT3

Li, T., Sun, F., Ji, X., Feng, Y., Rao, Z.

(2003) J Mol Biology 325: 1031-1037

Released	2003-08-26
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pyrococcus horikoshii
Macromolecule	HPhA (protein)
Unique Ligands	ACT, SO4

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1OZY \| pdb_00001ozy	Download File View File

Crystal Structure of Phospholipase A2 (MIPLA3) From Micropechis Ikaheka

Lok, S.M., Swaminathan, K.

(2005) FEBS J 272: 1211-1220

Released	2004-09-28
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Micropechis ikaheca
Macromolecule	PHOSPHOLIPASE A2 (protein)
Unique Ligands	SO4

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1P7O \| pdb_00001p7o	Download File View File

Crystal structure of phospholipase A2 (MIPLA4) from Micropechis ikaheka

Lok, S.M., Swaminathan, K.

(2005) FEBS J 272: 1211-1220

Released	2004-09-28
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Micropechis ikaheca
Macromolecule	PHOSPHOLIPASE A2 (protein)

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1PWO \| pdb_00001pwo	Download File View File

Crystal Structure of Phospholipase A2 (MIPLA2) from Micropechis Ikaheka

Lok, S.M., Swaminathan, K.

(2005) FEBS J 272: 1211-1220

Released	2005-03-01
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Micropechis ikaheca
Macromolecule	Phospholipase A2 (protein)

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1UDE \| pdb_00001ude	Download File View File

Crystal structure of the Inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Liu, B., Gao, R., Zhou, W., Bartlam, M., Rao, Z.

(2004) Biophys J 86: 420-427

Released	2004-01-20
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Inorganic pyrophosphatase (protein)

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1VE6 \| pdb_00001ve6	Download File View File

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1

Bartlam, M., Wang, G., Gao, R., Yang, H., Zhao, X., Xie, G., Cao, S., Feng, Y., Rao, Z.

(2004) Structure 12: 1481-1488

Released	2004-11-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Aeropyrum pernix
Macromolecule	Acylamino-acid-releasing enzyme (protein)
Unique Ligands	BOG, GOL

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1VE7 \| pdb_00001ve7	Download File View File

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1 in complex with p-nitrophenyl phosphate

Bartlam, M., Wang, G., Gao, R., Yang, H., Zhao, X., Xie, G., Cao, S., Feng, Y., Rao, Z.

(2004) Structure 12: 1481-1488

Released	2004-11-02
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Aeropyrum pernix
Macromolecule	Acylamino-acid-releasing enzyme (protein)
Unique Ligands	4NP, GOL

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2HU5 \| pdb_00002hu5	Download File View File

Binding of inhibitors by Acylaminoacyl-peptidase

Kiss, A.L., Hornung, B., Radi, K., Gengeliczki, Z., Sztaray, B., Harmat, V., Polgar, L.

(2007) J Mol Biology 368: 509-520

Released	2007-05-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Aeropyrum pernix
Macromolecule	Acylamino-acid-releasing enzyme (protein)
Unique Ligands	GLY, GOL, PHE

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2HU7 \| pdb_00002hu7	Download File View File

Binding of inhibitors by Acylaminoacyl peptidase

Kiss, A.L., Hornung, B., Radi, K., Gengeliczki, Z., Sztaray, B., Harmat, V., Polgar, L.

(2007) J Mol Biology 368: 509-520

Released	2007-05-15
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Aeropyrum pernix
Macromolecule	Acylamino-acid-releasing enzyme (protein)
Unique Ligands	ACE, GOL, PHE

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2HU8 \| pdb_00002hu8	Download File View File

Binding of inhibitors by Acylaminoacyl peptidase

Kiss, A.L., Hornung, B., Radi, K., Gengeliczki, Z., Sztaray, B., Harmat, V., Polgar, L.

(2007) J Mol Biology 368: 509-520

Released	2007-05-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Aeropyrum pernix
Macromolecule	Acylamino-acid-releasing enzyme (protein)
Unique Ligands	BE2, GLY, PHE

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3BYD \| pdb_00003byd	Download File View File

Crystal structure of beta-lactamase OXY-1-1 from Klebsiella oxytoca

Liang, Y.-H., Wu, S.W., Su, X.-D.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1460-1467

Released	2009-01-20
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Klebsiella oxytoca
Macromolecule	Beta-lactamase OXY-1 (protein)
Unique Ligands	ACT, SO4

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4F1H \| pdb_00004f1h	Download File View File

Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 1.662 Å
Organisms	Danio rerio
Macromolecule	Tyrosyl-DNA phosphodiesterase 2 (protein) DNA (5'-D(PTPGPCPAP*G)-3') (nucleic acid)
Unique Ligands	GOL, MG, PO4

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4F1I \| pdb_00004f1i	Download File View File

Crystal structure of SeMet TDP2 from Caenorhabditis elegans

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Caenorhabditis elegans
Macromolecule	5'-tyrosyl-DNA phosphodiesterase (protein)
Unique Ligands	GOL

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4FPV \| pdb_00004fpv	Download File View File

Crystal structure of D. rerio TDP2 complexed with single strand DNA product

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Danio rerio
Macromolecule	Tyrosyl-DNA phosphodiesterase 2 (protein) DNA (5'-D(PTPGPCPAP*G)-3') (nucleic acid)
Unique Ligands	GOL, MG, NA

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4FVA \| pdb_00004fva	Download File View File

Crystal structure of truncated Caenorhabditis elegans TDP2

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Caenorhabditis elegans
Macromolecule	5'-tyrosyl-DNA phosphodiesterase (protein)
Unique Ligands	EDO, MG, MLI

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4GEW \| pdb_00004gew	Download File View File

Crystal structure of TDP2 from C. elegans

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Caenorhabditis elegans
Macromolecule	5'-tyrosyl-DNA phosphodiesterase (protein)
Unique Ligands	GOL

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4PUQ \| pdb_00004puq	Download File View File

Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+

Schellenberg, M.J., Williams, R.S.

(2014) J Biological Chem 289: 17960-17969

Released	2014-05-14
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mus musculus
Macromolecule	Tyrosyl-DNA phosphodiesterase 2 (protein) DNA/RNA hybrid (hybrid)
Unique Ligands	ACT, GOL, MG

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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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6ADQ \| pdb_00006adq	Download File View File

Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis

Gong, H.R., Xu, A., Gao, R.G., Ji, W.X., Wang, S.H., Wang, Q., Li, J., Rao, Z.H.

(2018) Science 362:

Released	2018-11-14
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Mycolicibacterium smegmatis MC2 51
Macromolecule	Unique protein chains: 12
Unique Ligands	9XX, 9Y0, 9YF, CDL, CU, FES, HEA, HEC, HEM, MQ9, PLM

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6WGN \| pdb_00006wgn	Download File View File

Crystal structure of K-Ras(G12D) GppNHp bound to cyclic peptide ligand KD2

Zhang, Z., Gao, R., Hu, Q., Peacock, H., Peacock, D.M., Shokat, K.M., Suga, H.

(2020) ACS Cent Sci 6: 1753-1761

Released	2020-10-14
Method	X-RAY DIFFRACTION 1.601 Å
Organisms	Homo sapiens
Macromolecule	Cyclic Peptide KD2 (protein) GTPase KRas (protein)
Unique Ligands	GNP, MG

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7BPH \| pdb_00007bph	Download File View File

Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13

Hu, Q., Dai, S., Shokat, K.M.

(2022) Cell

Released	2021-03-31
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	GN13 (protein) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (protein)
Unique Ligands	CL, GNP, GOL, MG

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7BVC \| pdb_00007bvc	Download File View File

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol

Zhang, L., Zhao, Y., Gao, Y., Wang, Q., Li, J., Besra, G.S., Rao, Z.

(2020) Science 368: 1211-1219

Released	2020-04-29
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Integral membrane indolylacetylinositol arabinosyltransferase EmbA (protein) Integral membrane indolylacetylinositol arabinosyltransferase EmbB (protein) Meromycolate extension acyl carrier protein (protein)
Unique Ligands	95E, CA, CDL, F8L, PNS, PO4

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7BVE \| pdb_00007bve	Download File View File

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in complex with ethambutol

Zhang, L., Zhao, Y., Gao, Y., Wang, Q., Li, J., Besra, G.S., Rao, Z.

(2020) Science 368: 1211-1219

Released	2020-04-29
Method	ELECTRON MICROSCOPY 2.81 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Integral membrane indolylacetylinositol arabinosyltransferase EmbC (protein) Meromycolate extension acyl carrier protein (protein)
Unique Ligands	95E, CA, PN7, PO4

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7BVF \| pdb_00007bvf	Download File View File

Cryo-EM structure of Mycobacterium tuberculosis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol

Zhang, L., Zhao, Y., Gao, Y., Wang, Q., Li, J., Besra, G.S., Rao, Z.

(2020) Science 368: 1211-1219

Released	2020-04-29
Method	ELECTRON MICROSCOPY 2.97 Å
Organisms	Mycobacterium tuberculosis H37Rv Mycolicibacterium smegmatis MC2 155
Macromolecule	Meromycolate extension acyl carrier protein (protein) Probable arabinosyltransferase A (protein) Probable arabinosyltransferase B (protein)
Unique Ligands	95E, CA, CDL, DSL

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7BVG \| pdb_00007bvg	Download File View File

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.

Zhang, L., Zhao, Y., Gao, Y., Wang, Q., Li, J., Besra, G.S., Rao, Z.

(2020) Science 368: 1211-1219

Released	2020-04-29
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Integral membrane indolylacetylinositol arabinosyltransferase EmbA (protein) Integral membrane indolylacetylinositol arabinosyltransferase EmbB (protein) Meromycolate extension acyl carrier protein (protein)
Unique Ligands	CA, CDL, F8L, PNS, PO4
Unique branched monosaccharides	BXY

1 to 25 of 51 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

1KU5 | pdb_00001ku5

1OZY | pdb_00001ozy

1P7O | pdb_00001p7o

1PWO | pdb_00001pwo

1UDE | pdb_00001ude

1VE6 | pdb_00001ve6

1VE7 | pdb_00001ve7

2HU5 | pdb_00002hu5

2HU7 | pdb_00002hu7

2HU8 | pdb_00002hu8

3BYD | pdb_00003byd

4F1H | pdb_00004f1h

4F1I | pdb_00004f1i

4FPV | pdb_00004fpv

4FVA | pdb_00004fva

4GEW | pdb_00004gew

4PUQ | pdb_00004puq

5XS9 | pdb_00005xs9

6ADQ | pdb_00006adq

6WGN | pdb_00006wgn

7BPH | pdb_00007bph

7BVC | pdb_00007bvc

7BVE | pdb_00007bve

7BVF | pdb_00007bvf

7BVG | pdb_00007bvg