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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Pluta, R."

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	Homo sapiens (6)
	Streptococcus agalactiae (5)
	Danio rerio (4)
	Drosophila melanogaster (2)
	Xenopus laevis (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (13)
	Bacteria (5)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (18)

Polymer Entity Type

	Protein (18)
	DNA (16)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (2)
	1.5 - 2.0 (4)
	2.0 - 2.5 (8)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (5)
	2015 - 2019 (2)
	2020 - 2024 (11)

Symmetry Type

	Asymmetric (16)
	Cyclic (2)

SCOP Classification

Alpha and beta proteins (a/b) (1)

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1 to 18 of 18 Structures

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4LVI \| pdb_00004lvi	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 4.6

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTG oligonucleotide (nucleic acid)
Unique Ligands	GOL, MN

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4LVJ \| pdb_00004lvj	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 5.5

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTG oligonucleotide (nucleic acid)
Unique Ligands	ACT, MN

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4LVK \| pdb_00004lvk	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Phosphate). Mn-bound crystal structure at pH 4.6

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.37 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTGpo oligonucleotide (nucleic acid)
Unique Ligands	MN, NA

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4LVL \| pdb_00004lvl	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Thiophosphate). Mn-bound crystal structure at pH 6.8

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Streptococcus agalactiae synthetic construct
Macromolecule	Plasmid recombination enzyme (protein) DNA (5'-D(APCPTPTPTPAPT)-3') (nucleic acid) DNA (5'-D(APTPAPAPAPGPTPAPTPAPGPTPGPTPGP*(TS6))-3') (nucleic acid)
Unique Ligands	CL, MN

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4LVM \| pdb_00004lvm	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (23nt). Mn-bound crystal structure at pH 6.5

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTGT oligonucleotide (nucleic acid)
Unique Ligands	CL, MG, MN, NA

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6TBZ \| pdb_00006tbz	Download File View File

Crystal structure of the MH1 domain of Smad5-Smad3 chimera construct bound to the GGCGC site

Pluta, R., Macias, M.J.

(2021) Comput Struct Biotechnol J 19: 632-646

Released	2019-11-20
Method	X-RAY DIFFRACTION 1.782 Å
Organisms	Homo sapiens
Macromolecule	Mothers against decapentaplegic homolog 5 (protein) DNA (5'-D(PTPGPCPAPGPGPCPGPCPGPCPCPTPGPCPA)-3') (nucleic acid)
Unique Ligands	ZN

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6TCE \| pdb_00006tce	Download File View File

Crystal structure of the GGCT site-bound MH1 domain of Smad5 containing a GGGS insertion in the Loop1

Pluta, R., Macias, M.J.

(2021) Comput Struct Biotechnol J 19: 632-646

Released	2019-11-20
Method	X-RAY DIFFRACTION 2.92 Å
Organisms	Homo sapiens
Macromolecule	Mothers against decapentaplegic homolog 5 (protein) DNA (5'-D(PTPGPCPAPGPGPCPTPAPGPCPCPTPGPCPA)-3') (nucleic acid)
Unique Ligands	ZN

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6Z7O \| pdb_00006z7o	Download File View File

Crystal structure of Thioredoxin T from Drosophila melanogaster

Freier, R., Aragon, E., Baginski, B., Pluta, R., Martin-Malpartida, P., Torner, C., Gonzaez, C., Macias, M.

(2021) IUCrJ 8: 281-294

Released	2020-10-21
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Drosophila melanogaster
Macromolecule	Thioredoxin-T (protein)
Unique Ligands	ZN

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6ZMN \| pdb_00006zmn	Download File View File

Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site

Pluta, R., Macias, M.J.

(2021) Comput Struct Biotechnol J 19: 632-646

Released	2020-08-26
Method	X-RAY DIFFRACTION 2.333 Å
Organisms	Homo sapiens
Macromolecule	Mothers against decapentaplegic homolog 3 (protein) DNA (5'-D(PTPGPCPAPGPGPCPGPCPGPCPCPTPGPCPA)-3') (nucleic acid)
Unique Ligands	ACT, EDO, PGE, ZN

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6ZMU \| pdb_00006zmu	Download File View File

Crystal structure of the germline-specific thioredoxin protein Deadhead (Thioredoxin-1) from Drospohila melanogaster, P43212

Baginski, B., Pluta, R., Macias, M.J.

(2021) IUCrJ 8: 281-294

Released	2020-10-21
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Drosophila melanogaster
Macromolecule	Thioredoxin-1 (protein)
Unique Ligands	NA, SO4

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7YZ7 \| pdb_00007yz7	Download File View File

Crystal structure of the zebrafish FoxH1 bound to the TGTGGATT site

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 0.98 Å
Organisms	Danio rerio
Macromolecule	Forkhead box protein H1 (protein) DNA (5'-D(APGPAPTPTPGPTPGPGPAPTPTPGPAPGPA)-3') (nucleic acid) DNA (5'-D(TPCPTPCPAPAPTPCPCPAPCPAPAPTPCPT)-3') (nucleic acid)
Unique Ligands	K

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7YZA \| pdb_00007yza	Download File View File

Crystal structure of the zebrafish FoxH1 bound to the TGTGTATT site

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 1.18 Å
Organisms	Danio rerio
Macromolecule	Forkhead box protein H1 (protein) DNA (5'-D(APGPAPTPTPGPTPGPTPAPTPTPGPAPGPA)-3') (nucleic acid) DNA (5'-D(TPCPTPCPAPAPTPAPCPAPCPAPAPTPCPT)-3') (nucleic acid)
Unique Ligands	K

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7YZB \| pdb_00007yzb	Download File View File

Crystal structure of the human FoxH1 bound to the TGTGGATT site

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	Homo sapiens
Macromolecule	Forkhead box protein H1 (protein) DNA (5'-D(APGPAPTPTPGPTPGPGPAPTPTPGPCPGPA)-3') (nucleic acid) DNA (5'-D(TPCPGPCPAPAPTPCPCPAPCPAPAPTPCPT)-3') (nucleic acid)
Unique Ligands	K

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7YZC \| pdb_00007yzc	Download File View File

Crystal structure of the zebrafish FoxH1 bound to the TGTTTATT site

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Danio rerio
Macromolecule	Forkhead box protein H1 (protein) DNA (5'-D(APGPAPTPTPGPTPTPTPAPTPTPGPAPGPA)-3') (nucleic acid) DNA (5'-D(TPCPTPCPAPAPTPAPAPAPCPAPAPTPCPT)-3') (nucleic acid)
Unique Ligands	ACT

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7YZD \| pdb_00007yzd	Download File View File

Crystal structure of the zebrafish FoxH1 bound to the TGTTTACT site (fkh motif GTAAACA)

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 2.13 Å
Organisms	Danio rerio
Macromolecule	Forkhead box protein H1 (protein) DNA (5'-D(TPCPTPCPAPGPTPAPAPAPCPAPAPTPCPT)-3') (nucleic acid) DNA (5'-D(PAPGPAPTPTPGPTPTPTPAPCPTPGPAPGPA)-3') (nucleic acid)
Unique Ligands	ACT, PGE

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7YZE \| pdb_00007yze	Download File View File

Crystal structure of the human FoxA2 bound to the TGTTTACT site (forkhead motif GTAAACA)

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens
Macromolecule	Hepatocyte nuclear factor 3-beta (protein) DNA (5'-D(APGPAPTPTPGPTPTPTPAPCPTPGPAPGPA)-3') (nucleic acid) DNA (5'-D(TPCPTPCPAPGPTPAPAPAPCPAPAPTPCPT)-3') (nucleic acid)
Unique Ligands	K, SO4

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7YZF \| pdb_00007yzf	Download File View File

Crystal structure of the human FoxA2 bound to the TGTTTATT site (forkhead motif ATAAACA)

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Homo sapiens
Macromolecule	Hepatocyte nuclear factor 3-beta (protein) DNA (5'-D(PAPGPAPTPTPGPTPTPTPAPTPTPGPAPGPA)-3') (nucleic acid) DNA (5'-D(PTPCPTPCPAPAPTPAPAPAPCPAPAPTPCPT)-3') (nucleic acid)
Unique Ligands	K

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7YZG \| pdb_00007yzg	Download File View File

Crystal structure of the Xenopus FoxH1 bound to the TGTGGATT site

Pluta, R., Macias, M.J.

(2022) Nat Commun 13: 7279-7279

Released	2022-11-16
Method	X-RAY DIFFRACTION 2.82 Å
Organisms	Xenopus laevis
Macromolecule	Forkhead box protein H1 (protein) DNA (5'-D(CPAPGPAPTPTPGPTPGPGPAPTPTPGPAPG)-3') (nucleic acid) DNA (5'-D(CPTPCPAPAPTPCPCPAPCPAPAPTPCPTPG)-3') (nucleic acid)

1 to 18 of 18 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

4LVI | pdb_00004lvi

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 4.6

4LVJ | pdb_00004lvj

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 5.5

4LVK | pdb_00004lvk

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Phosphate). Mn-bound crystal structure at pH 4.6

4LVL | pdb_00004lvl

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Thiophosphate). Mn-bound crystal structure at pH 6.8

4LVM | pdb_00004lvm

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (23nt). Mn-bound crystal structure at pH 6.5

6TBZ | pdb_00006tbz

Crystal structure of the MH1 domain of Smad5-Smad3 chimera construct bound to the GGCGC site

6TCE | pdb_00006tce

Crystal structure of the GGCT site-bound MH1 domain of Smad5 containing a GGGS insertion in the Loop1

6Z7O | pdb_00006z7o

Crystal structure of Thioredoxin T from Drosophila melanogaster

6ZMN | pdb_00006zmn

Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site

6ZMU | pdb_00006zmu

Crystal structure of the germline-specific thioredoxin protein Deadhead (Thioredoxin-1) from Drospohila melanogaster, P43212

7YZ7 | pdb_00007yz7

Crystal structure of the zebrafish FoxH1 bound to the TGTGGATT site

7YZA | pdb_00007yza

Crystal structure of the zebrafish FoxH1 bound to the TGTGTATT site

7YZB | pdb_00007yzb

Crystal structure of the human FoxH1 bound to the TGTGGATT site

7YZC | pdb_00007yzc

Crystal structure of the zebrafish FoxH1 bound to the TGTTTATT site

7YZD | pdb_00007yzd

Crystal structure of the zebrafish FoxH1 bound to the TGTTTACT site (fkh motif GTAAACA)

7YZE | pdb_00007yze

Crystal structure of the human FoxA2 bound to the TGTTTACT site (forkhead motif GTAAACA)

7YZF | pdb_00007yzf

Crystal structure of the human FoxA2 bound to the TGTTTATT site (forkhead motif ATAAACA)

7YZG | pdb_00007yzg

Crystal structure of the Xenopus FoxH1 bound to the TGTGGATT site

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

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Refinement Resolution (Å)

Release Date

Symmetry Type

SCOP Classification

4LVI | pdb_00004lvi

4LVJ | pdb_00004lvj

4LVK | pdb_00004lvk

4LVL | pdb_00004lvl

4LVM | pdb_00004lvm

6TBZ | pdb_00006tbz

6TCE | pdb_00006tce

6Z7O | pdb_00006z7o

6ZMN | pdb_00006zmn

6ZMU | pdb_00006zmu

7YZ7 | pdb_00007yz7

7YZA | pdb_00007yza

7YZB | pdb_00007yzb

7YZC | pdb_00007yzc

7YZD | pdb_00007yzd

7YZE | pdb_00007yze

7YZF | pdb_00007yzf

7YZG | pdb_00007yzg