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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Expression Organism = "synthetic construct"

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Search Summary

This query matches 381 Structures.

Refinements

Structure Determination Methodology

experimental (381)

Scientific Name of Source Organism

	synthetic construct (186)
	Homo sapiens (153)
	Xenopus laevis (24)
	Escherichia coli (17)
	Mus musculus (17)
	Saccharomyces cerevisiae S288C (14)
	Rattus norvegicus (12)
	Saccharomyces cerevisiae (12)
	Tetrahymena thermophila (10)
	unidentified (9)

More...

Taxonomy

	Eukaryota (241)
	other sequences (190)
	Bacteria (73)
	Riboviria (41)
	unclassified sequences (14)
	Archaea (4)
	Varidnaviria (4)
	Duplodnaviria (3)
	Monodnaviria (3)

Experimental Method

	X-RAY DIFFRACTION (217)
	ELECTRON MICROSCOPY (136)
	SOLUTION NMR (27)
	SOLID-STATE NMR (1)

Polymer Entity Type

	Protein (328)
	DNA (154)
	RNA (104)
	NA-hybrid (2)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (22)
	1.5 - 2.0 (48)
	2.0 - 2.5 (75)
	2.5 - 3.0 (81)
	3.0 - 3.5 (65)
	3.5 - 4.0 (30)
	4.0 - 4.5 (9)
	> 4.5 (21)

Release Date

	2005 - 2009 (4)
	2010 - 2014 (1)
	2015 - 2019 (144)
	2020 - 2024 (201)
	2025 - 2029 (31)

Enzyme Classification Name

	Transferases (73)
	Hydrolases (69)
	Isomerases (23)
	Lyases (12)
	Oxidoreductases (7)
	Translocases (1)

Membrane Protein Annotation

	PDBTM (11)
	OPM (9)
	mpstruc (5)
	MemProtMD (4)

Symmetry Type

	Asymmetric (251)
	Cyclic (67)
	Dihedral (6)
	Helical (5)
	Icosahedral (1)

SCOP Classification

	All beta proteins (32)
	All alpha proteins (32)
	Alpha and beta proteins (a+b) (25)
	Artifacts (21)
	Alpha and beta proteins (a/b) (4)
	Designed proteins (1)
	Multi-domain proteins (alpha and beta) (1)
	Small proteins (1)

AllSelected

1 to 25 of 381 Structures

Page 1 of 16

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2D7Q \| pdb_00002d7q	Download File View File

Solution structure of the 23th Filamin domain from human Filamin C

Tomizawa, T., Kigawa, T., Koshiba, S., Inoue, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-11-24
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Filamin-C (protein)

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2D9J \| pdb_00002d9j	Download File View File

Solution structure of the RGS domain of Regulator of G-protein signaling 7

Zhang, H.P., Nagasima, T., Hayashi, F., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-12-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Regulator of G-protein signalling 7 (protein)

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2DAO \| pdb_00002dao	Download File View File

Solution structure of ETS domain Transcriptional factor ETV6 protein

Niraula, T.N., Sasagawa, A., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-12-12
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Transcription factor ETV6 (protein)

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2OSL \| pdb_00002osl	Download File View File

Crystal structure of Rituximab Fab in complex with an epitope peptide

Du, J., Zhong, C., Ding, J.

(2007) J Biological Chem 282: 15073-15080

Released	2007-04-10
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	B-lymphocyte antigen CD20 (protein) heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragment (protein) light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragment (protein)

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4WDI \| pdb_00004wdi	Download File View File

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Rizkallah, P.J., Cole, D.K.

(2015) J Biological Chem 290: 18924-18933

Released	2015-06-24
Method	X-RAY DIFFRACTION 2.313 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Beta-2-microglobulin (protein) H-2 class I histocompatibility antigen, K-D alpha chain (protein) Insulin (protein)
Unique Ligands	EDO, SO4

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4WHT \| pdb_00004wht	Download File View File

Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody 3/11, P1 crystal form

Krey, T., Rey, F.A.

(2015) J Virol 89: 2170-2181

Released	2014-12-17
Method	X-RAY DIFFRACTION 2.22 Å
Organisms	Hepacivirus hominis Rattus norvegicus
Macromolecule	Epitope peptide (protein) Heavy chain of the Fab fragment derived from neutralizing antibody 3/11 (protein) Light chain of the Fab fragment derived from neutralizing antibody 3/11 (protein)

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4WY7 \| pdb_00004wy7	Download File View File

Crystal structure of recombinant 4E10 expressed in Escherichia coli with epitope bound

Rujas, E., Morante, K., Tsumoto, K., Nieva, J.L., Caaveiro, J.M.M.

(2015) J Biological Chem 290: 12999-13015

Released	2015-03-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens Human immunodeficiency virus type 1 (WMJ2 ISOLATE)
Macromolecule	Envelope glycoprotein gp160 (protein) Fab 4E10 Heavy chain (protein) Fab 4E10Light chain (protein)
Unique Ligands	GOL

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4WZJ \| pdb_00004wzj	Download File View File

Spliceosomal U4 snRNP core domain

Leung, A.K.W., Nagai, K., Li, J.

(2011) Nature 473: 536-539

Released	2015-01-14
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 1

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4X3E \| pdb_00004x3e	Download File View File

Crystal structure of EED in complex with a trimethylated Jarid2 peptide

Justin, N., Gamblin, S.J., Margueron, R.

(2015) Mol Cell 57: 769-783

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	ALA-GLN-ARG-M3L-PHE-ALA-GLN-SER (protein) Polycomb protein EED (protein)

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4XCO \| pdb_00004xco	Download File View File

Signal-sequence induced conformational changes in the signal recognition particle

Hainzl, T., Sauer-Eriksson, A.E.

(2015) Nat Commun 6: 7163-7163

Released	2015-06-10
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Signal recognition particle 19 kDa protein (protein) Signal recognition particle 54 kDa protein,signal sequence (protein) RNA (nucleic acid)
Unique Ligands	MG, NA

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4XQZ \| pdb_00004xqz	Download File View File

Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by chloride and MES

Rohner, M., Medina-Molner, A., Spingler, B.

(2016) Inorg Chem 55: 6130-6140

Released	2016-01-27
Method	X-RAY DIFFRACTION 2.151 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(CPGPCPGPCPG)-3') (nucleic acid)
Unique Ligands	CA, CL, CU, MES, MOH

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4YIR \| pdb_00004yir	Download File View File

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA

Min, J.-H., Chen, X., Kim, Y.

(2015) Nat Commun 6: 5849

Released	2015-03-11
Method	X-RAY DIFFRACTION 3.0501 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	DNA repair protein RAD4 (protein) UV excision repair protein RAD23 (protein) DNA (5'-D(APTPTPGPTPAPGPCPGGPGPGPAPTPGPTPCPGPAPGPTPCPA)-3') (nucleic acid) DNA (5'-D(TPTPGPAPCPTPCP(G47)PAPCPAPTPCPCPCPCPCPGPCPTPAPCPAP*A)-3') (nucleic acid)

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4Z76 \| pdb_00004z76	Download File View File

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Rizkallah, P.J., Cole, D.K.

(2015) J Biological Chem 290: 18924-18933

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Beta-2-microglobulin (protein) H-2 class I histocompatibility antigen, K-D alpha chain (protein) Insulin (protein)
Unique Ligands	EDO, GOL, SO4

Explore in 3D

4Z77 \| pdb_00004z77	Download File View File

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Rizkallah, P.J., Cole, D.K.

To be published

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Beta-2-microglobulin (protein) H-2 class I histocompatibility antigen, K-D alpha chain (protein) Insulin (protein)
Unique Ligands	15P, EDO, GOL, SO4

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4Z78 \| pdb_00004z78	Download File View File

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Rizkallah, P.J., Cole, D.K.

(2015) J Biological Chem 290: 18924-18933

Released	2015-06-24
Method	X-RAY DIFFRACTION 2.304 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Beta-2-microglobulin (protein) H-2 class I histocompatibility antigen, K-D alpha chain (protein) Insulin (protein)
Unique Ligands	EDO, GOL, SO4

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4ZTJ \| pdb_00004ztj	Download File View File

Crystal Structure of the Prototype Foamy Virus Intasome with a 2-Pyridinone Aminal Inhibitor

Klein, D.J., Patel, S.

(2015) J Med Chem 58: 8154-8165

Released	2015-10-07
Method	X-RAY DIFFRACTION 2.67 Å
Organisms	Human spumaretrovirus
Macromolecule	PFV INTEGRASE (protein) DNA (5'-D(APTPTPGPTPCPAPTPGPGPAPAPTPTPTPCPGPCPA)-3') (nucleic acid) DNA (5'-D(TPGPCPGPAPAPAPTPTPCPCPAPTPGPAPCPA)-3') (nucleic acid)
Unique Ligands	4RT, GOL, MG, SO4, ZN

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5BTA \| pdb_00005bta	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	MFX, MG

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5BTC \| pdb_00005btc	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	CPF, MG

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5BTD \| pdb_00005btd	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.497 Å
Organisms	Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	GFN, MG

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5BTF \| pdb_00005btf	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	GFN, MG

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5BTG \| pdb_00005btg	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	LFX, MG

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5BTI \| pdb_00005bti	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.501 Å
Organisms	Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	LFX, MG

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5BTL \| pdb_00005btl	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	8MX, MG

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5BTN \| pdb_00005btn	Download File View File

Crystal structure of a topoisomerase II complex

Blower, T.R., Williamson, B.H., Kerns, R.J., Berger, J.M.

(2016) Proc Natl Acad Sci U S A 113: 1706-1713

Released	2016-03-02
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mycobacterium tuberculosis H37Rv synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA (nucleic acid) DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC (nucleic acid)
Unique Ligands	8MX, MG

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5CBX \| pdb_00005cbx	Download File View File

AncGR DNA Binding Domain - (+)GRE Complex

Hudson, W.H., Ortlund, E.A.

(2016) Proc Natl Acad Sci U S A 113: 326-331

Released	2015-12-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	synthetic construct unidentified
Macromolecule	AncGR DNA Binding Domain (protein) DNA (5'-D(CPCPAPGPAPAPCPAPGPAPGPTPGPTPTPCPTPG)-3') (nucleic acid) DNA (5'-D(TPCPAPGPAPAPCPAPCPTPCPTPGPTPTPCPTPG)-3') (nucleic acid)
Unique Ligands	ZN

1 to 25 of 381 Structures

Page 1 of 16

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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

2D7Q | pdb_00002d7q

2D9J | pdb_00002d9j

2DAO | pdb_00002dao

2OSL | pdb_00002osl

4WDI | pdb_00004wdi

4WHT | pdb_00004wht

4WY7 | pdb_00004wy7

4WZJ | pdb_00004wzj

4X3E | pdb_00004x3e

4XCO | pdb_00004xco

4XQZ | pdb_00004xqz

4YIR | pdb_00004yir

4Z76 | pdb_00004z76

4Z77 | pdb_00004z77

4Z78 | pdb_00004z78

4ZTJ | pdb_00004ztj

5BTA | pdb_00005bta

5BTC | pdb_00005btc

5BTD | pdb_00005btd

5BTF | pdb_00005btf

5BTG | pdb_00005btg

5BTI | pdb_00005bti

5BTL | pdb_00005btl

5BTN | pdb_00005btn

5CBX | pdb_00005cbx