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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ma, B."

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Search Summary

This query matches 95 Structures.

Refinements

Structure Determination Methodology

experimental (95)

Scientific Name of Source Organism

	Homo sapiens (66)
	Venezuelan equine encephalitis virus (strain TC-83) (6)
	Bos taurus (4)
	Eastern equine encephalitis virus (4)
	Mus musculus (4)
	Trichoderma reesei (4)
	Escherichia coli (3)
	Streptomyces avermitilis MA-4680 = NBRC 14893 (3)
	Helicobacter pylori 26695 (2)
	Methanococcus maripaludis (2)

More...

Taxonomy

	Eukaryota (79)
	Riboviria (14)
	Bacteria (12)
	Archaea (2)
	Duplodnaviria (1)
	Varidnaviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (57)
	ELECTRON MICROSCOPY (33)
	SOLUTION NMR (4)
	SOLID-STATE NMR (1)

Polymer Entity Type

	Protein (95)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (21)
	2.0 - 2.5 (17)
	2.5 - 3.0 (9)
	3.0 - 3.5 (15)
	3.5 - 4.0 (6)
	> 4.5 (16)

Release Date

	2010 - 2014 (10)
	2015 - 2019 (25)
	2020 - 2024 (60)

Enzyme Classification Name

	Transferases (26)
	Hydrolases (24)
	Ligases (8)

Membrane Protein Annotation

	OPM (7)
	MemProtMD (2)
	PDBTM (1)

Symmetry Type

	Asymmetric (71)
	Cyclic (16)
	Dihedral (6)
	Icosahedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (11)
	Alpha and beta proteins (a/b) (6)
	All beta proteins (5)
	All alpha proteins (3)
	Artifacts (2)
	Small proteins (1)

AllSelected

1 to 25 of 95 Structures

Page 1 of 4

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2MXU \| pdb_00002mxu	Download File View File

42-Residue Beta Amyloid Fibril

Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R., Ishii, Y.

(2015) Nat Struct Mol Biol 22: 499-505

Released	2015-05-06
Method	SOLID-STATE NMR
Organisms	Homo sapiens
Macromolecule	Amyloid beta A4 protein (protein)

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3J02 \| pdb_00003j02	Download File View File

Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state

Zhang, J., Ma, B., DiMaio, F., Douglas, N.R., Joachimiak, L., Baker, D., Frydman, J., Levitt, M., Chiu, W.

(2011) Structure 19: 633-639

Released	2011-05-18
Method	ELECTRON MICROSCOPY 8 Å
Organisms	Methanococcus maripaludis
Macromolecule	Lidless D386A Mm-cpn variant (protein)

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3J03 \| pdb_00003j03	Download File View File

Lidless Mm-cpn in the closed state with ATP/AlFx

Zhang, J., Ma, B., DiMaio, F., Douglas, N.R., Joachimiak, L., Baker, D., Frydman, J., Levitt, M., Chiu, W.

(2011) Structure 19: 633-639

Released	2011-05-18
Method	ELECTRON MICROSCOPY 4.8 Å
Organisms	Methanococcus maripaludis
Macromolecule	Lidless Mm-cpn (protein)

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4A0O \| pdb_00004a0o	Download File View File

Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 10.5 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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4A0V \| pdb_00004a0v	Download File View File

model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 10.7 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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4A0W \| pdb_00004a0w	Download File View File

model built against symmetry-free cryo-EM map of TRiC-ADP-AlFx

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 13.9 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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4A13 \| pdb_00004a13	Download File View File

model refined against symmetry-free cryo-EM map of TRiC-ADP

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 11.3 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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4EYA \| pdb_00004eya	Download File View File

Crystal Structure of a Plectonemic RNA Supercoil

Stagno, J.R., Ji, X.

(2012) Nat Commun 3: 901-901

Released	2012-06-20
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Aquifex aeolicus VF5 synthetic construct
Macromolecule	N utilization substance protein B homolog (protein) RNA (5'-R(GPGPCPUPCPCPUPUPGPGPCPA)-3') (nucleic acid)
Unique Ligands	GOL, SO4

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4G0N \| pdb_00004g0n	Download File View File

Crystal Structure of wt H-Ras-GppNHp bound to the RBD of Raf Kinase

Fetics, S.K., Kearney, B.M., Buhrman, G., Mattos, C.

(2015) Structure 23: 505-516

Released	2013-07-17
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens
Macromolecule	GTPase HRas (protein) RAF proto-oncogene serine/threonine-protein kinase (protein)
Unique Ligands	ACT, CA, DTU, GNP, MG

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4G3X \| pdb_00004g3x	Download File View File

Crystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase

Fetics, S.K., Kearney, B.M., Buhrman, G., Mattos, C.

(2015) Structure 23: 505-516

Released	2013-07-17
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Homo sapiens
Macromolecule	GTPase HRas (protein) RAF proto-oncogene serine/threonine-protein kinase (protein)
Unique Ligands	GNP, MG

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4V94 \| pdb_00004v94	Download File View File

Molecular architecture of the eukaryotic chaperonin TRiC/CCT derived by a combination of chemical crosslinking and mass-spectrometry, XL-MS

Leitner, A., Joachimiak, L.A., Bracher, A., Walzthoeni, T., Chen, B., Monkemeyer, L., Pechmann, S., Holmes, S., Cong, Y., Ma, B., Ludtke, S., Chiu, W., Hartl, F.U., Aebersold, R., Frydman, J.

(2012) Structure 20: 814-825

Released	2014-07-09
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 8
Unique Ligands	ADP, BEF, MG

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5DH4 \| pdb_00005dh4	Download File View File

PDE10 complexed with 5-chloro-N-[(2,4-dimethylthiazol-5-yl)methyl]pyrazolo[1,5-a]pyrimidin-7-amine

Yan, Y.

(2016) Bioorg Med Chem Lett 26: 126-132

Released	2016-01-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (protein)
Unique Ligands	4PX, 5AV, MG, ZN

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5DH5 \| pdb_00005dh5	Download File View File

PDE10 complexed with N-[(1-methylpyrazol-4-yl)methyl]-5-[[(1S,2S)-2-(2-pyridyl)cyclopropyl]methoxy]pyrazolo[1,5-a]pyrimidin-7-amine

Yan, Y.

(2016) Bioorg Med Chem Lett 26: 126-132

Released	2016-01-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (protein)
Unique Ligands	5AY, MG, ZN

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5F6D \| pdb_00005f6d	Download File View File

Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6

Lountos, G.T., Hewitt, W.M., Zlotkowski, K., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.553 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein)
Unique Ligands	5VJ

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5F6E \| pdb_00005f6e	Download File View File

Crystal Structure of human Ubc9 (K48A/K49A/E54A)

Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.12 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein)
Unique Ligands	EDO

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5F6U \| pdb_00005f6u	Download File View File

Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)

Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.552 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein)
Unique Ligands	5VK

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5F6V \| pdb_00005f6v	Download File View File

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from fragment cocktail screen)

Lountos, G.T., Hewitt, W.M., Zlotkowski, K., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.492 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein)
Unique Ligands	5VL

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5F6W \| pdb_00005f6w	Download File View File

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol)

Lountos, G.T., Hewitt, W.M., Zlotkowski, K., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.699 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein)
Unique Ligands	5VL

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5F6X \| pdb_00005f6x	Download File View File

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen)

Lountos, G.T., Hewitt, W.M., Zlotkowski, K., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein)
Unique Ligands	5VM

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5F6Y \| pdb_00005f6y	Download File View File

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)

Lountos, G.T., Hewitt, W.M., Zlotkowski, K., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.14 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein)
Unique Ligands	5VM

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5HEK \| pdb_00005hek	Download File View File

crystal structure of M1.HpyAVI

Ma, B., Zhang, H., Liu, W.

(2016) Oncotarget 7: 40965-40977

Released	2016-11-16
Method	X-RAY DIFFRACTION 3 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Adenine specific DNA methyltransferase (DpnA) (protein)

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5HFJ \| pdb_00005hfj	Download File View File

crystal structure of M1.HpyAVI-SAM complex

Ma, B., Liu, W., Zhang, H.

(2016) Oncotarget 7: 40965-40977

Released	2016-11-16
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Adenine specific DNA methyltransferase (DpnA) (protein)
Unique Ligands	SAM

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5KNJ \| pdb_00005knj	Download File View File

Pseudokinase Domain of MLKL bound to Compound 1.

Marcotte, D.J.

(2016) PLoS One 11: e0165983-e0165983

Released	2016-11-16
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Homo sapiens
Macromolecule	Mixed lineage kinase domain-like protein (protein)
Unique Ligands	6UX

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5KO1 \| pdb_00005ko1	Download File View File

Pseudokinase Domain of MLKL bound to Compound 4.

Marcotte, D.J.

(2016) PLoS One 11: e0165983-e0165983

Released	2016-11-16
Method	X-RAY DIFFRACTION 2.16 Å
Organisms	Homo sapiens
Macromolecule	Mixed lineage kinase domain-like protein (protein)
Unique Ligands	6UY