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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "DNA-BINDING PROTEIN/DNA"

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Search Summary

This query matches 1,235 Structures.

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Structure Determination Methodology

experimental (1,235)

Scientific Name of Source Organism

	Homo sapiens (527)
	synthetic construct (450)
	Escherichia coli (106)
	Escherichia coli K-12 (85)
	Mus musculus (56)
	Xenopus laevis (54)
	Saccharomyces cerevisiae (43)
	Arabidopsis thaliana (28)
	Saccharomyces cerevisiae S288C (25)
	Xanthomonas campestris pv. armoraciae (23)

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Taxonomy

	Eukaryota (746)
	other sequences (450)
	Bacteria (415)
	Archaea (47)
	Duplodnaviria (26)
	unclassified sequences (19)
	Varidnaviria (13)
	Riboviria (11)
	Monodnaviria (9)

Experimental Method

	X-RAY DIFFRACTION (889)
	ELECTRON MICROSCOPY (314)
	SOLUTION NMR (32)

Polymer Entity Type

	Protein (1,235)
	DNA (1,220)
	RNA (47)
	NA-hybrid (6)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (157)
	2.0 - 2.5 (300)
	2.5 - 3.0 (324)
	3.0 - 3.5 (242)
	3.5 - 4.0 (99)
	4.0 - 4.5 (34)
	> 4.5 (40)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (27)
	2000 - 2004 (39)
	2005 - 2009 (56)
	2010 - 2014 (190)
	2015 - 2019 (272)
	2020 - 2024 (597)
	2025 - 2029 (51)

Enzyme Classification Name

	Hydrolases (226)
	Transferases (190)
	Lyases (109)
	Isomerases (21)
	Oxidoreductases (10)
	Ligases (11)

Symmetry Type

	Asymmetric (835)
	Cyclic (373)
	Helical (24)
	Dihedral (12)
	Octahedral (3)

SCOP Classification

	All alpha proteins (107)
	All beta proteins (46)
	Artifacts (32)
	Alpha and beta proteins (a+b) (28)
	Alpha and beta proteins (a/b) (5)
	Small proteins (6)
	Peptides (4)
	Designed proteins (1)

AllSelected

1 to 25 of 1,235 Structures

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1AHD \| pdb_00001ahd	Download File View File

DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX

Billeter, M., Qian, Y.Q., Otting, G., Muller, M., Gehring, W.J., Wuthrich, K.

(1993) J Mol Biology 234: 1084-1097

Released	1993-10-31
Method	SOLUTION NMR
Organisms	Drosophila subobscura
Macromolecule	Homeotic protein antennapedia (protein) DNA (5'-D(CPTPCPTPAPAPTPGPGPCPTPTPTPC)-3') (nucleic acid) DNA (5'-D(GPAPAPAPGPCPCPAPTPTPAPGPAPG)-3') (nucleic acid)

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1AKH \| pdb_00001akh	Download File View File

MAT A1/ALPHA2/DNA TERNARY COMPLEX

Li, T., Jin, Y., Vershon, A.K., Wolberger, C.

(1998) Nucleic Acids Res 26: 5707-5718

Released	1998-05-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROTEIN (MATING-TYPE PROTEIN A-1) (protein) PROTEIN (MATING-TYPE PROTEIN ALPHA-2) (protein) DNA (5'-D(TPAPCPAPTPGPTPAPAPAPAPAPTPTPTPAPC PAPTPCPA)-3') (nucleic acid) DNA (5'-D(TPAPTPGPAPTPGPTPAPAPAPTPTPTPTPTPA PCPAPTPG)-3') (nucleic acid)

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1AOI \| pdb_00001aoi	Download File View File

COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT

Luger, K., Maeder, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J.

(1997) Nature 389: 251-260

Released	1998-09-30
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Xenopus laevis
Macromolecule	HISTONE H2A (protein) HISTONE H2B (protein) HISTONE H3 (protein) HISTONE H4 (protein) PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA (nucleic acid)
Unique Ligands	MN

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1APL \| pdb_00001apl	Download File View File

CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS

Wolberger, C., Vershon, A.K., Liu, B., Johnson, A.D., Pabo, C.O.

(1991) Cell 67: 517-528

Released	1993-10-21
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROTEIN (MAT-ALPHA2 HOMEODOMAIN) (protein) DNA (5'-D(APCPAPTPGPTPAPAPTPTPCPAPTPTPTPAPC PAPCPGPC)-3') (nucleic acid) DNA (5'-D(TPGPCPGPTPGPTPAPAPAPTPGPAPAPTPTPA PCPAPTPG)-3') (nucleic acid)

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1AZP \| pdb_00001azp	Download File View File

HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX

Robinson, H., Gao, Y.-G., Mccrary, B.S., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

(1998) Nature 392: 202-205

Released	1999-01-13
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Sulfolobus acidocaldarius
Macromolecule	PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D) (protein) DNA (5'-D(GPCPGPAPTPCPGPC)-3') (nucleic acid)

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1AZQ \| pdb_00001azq	Download File View File

HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX

Robinson, H., Gao, Y.-G., Mccrary, B.S., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

(1998) Nature 392: 202-205

Released	1999-01-13
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Sulfolobus acidocaldarius
Macromolecule	PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D) (protein) DNA (5'-D(GPTPAPAPTPTPAPC)-3') (nucleic acid)

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1BBX \| pdb_00001bbx	Download File View File

NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE

Agback, P., Baumann, H., Knapp, S., Ladenstein, R., Hard, T.

(1998) Nat Struct Biol 5: 579-584

Released	1998-10-14
Method	SOLUTION NMR
Organisms	Saccharolobus solfataricus
Macromolecule	DNA-BINDING PROTEIN 7D (protein) DNA (5'-D(CPTPAPGPCPGPCPGPCPTPAPG)-3') (nucleic acid)

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1BF4 \| pdb_00001bf4	Download File View File

CHROMOSOMAL DNA-BINDING PROTEIN SSO7D/D(GCGAACGC) COMPLEX

Su, S., Gao, Y.-G., Robinson, H., Padmanabhan, S., Lim, L., Shriver, J.W., Wang, A.H.-J.

(1998) Nat Struct Biol 5: 782-786

Released	1999-11-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Sulfolobus acidocaldarius
Macromolecule	PROTEIN (CHROMOSOMAL PROTEIN SSO7D) (protein) DNA (5'-D(GPCPGPAPAPCPGPC)-3') (nucleic acid) DNA (5'-D(GPCPGPTP5IUPCPGPC)-3') (nucleic acid)

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1BNZ \| pdb_00001bnz	Download File View File

SSO7D HYPERTHERMOPHILE PROTEIN/DNA COMPLEX

Gao, Y.-G., Su, S.-Y., Robinson, H., Padmanabhan, S., Lim, L., Mccrary, B.S., Edmondos, S.P., Shrive, J.W., Wang, A.H.-J.

(1998) Nat Struct Biol 5: 782-786

Released	1998-11-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sulfolobus acidocaldarius
Macromolecule	DNA-BINDING PROTEIN 7A (protein) 5'-D(GPTPAPAPTPTPAPC)-3' (nucleic acid)

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1C8C \| pdb_00001c8c	Download File View File

CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS

Su, S., Gao, Y.-G., Robinson, H., Liaw, Y.-C., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

(2000) J Mol Biology 303: 395-403

Released	2001-05-04
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA-BINDING PROTEIN 7A (protein) 5'-D(GPTPGPAPTPCPGPC)-3' (nucleic acid)

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1GDT \| pdb_00001gdt	Download File View File

CRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA-DELTA RESOLVASE COMPLEXED WITH A 34 BP CLEAVAGE SITE

Yang, W., Steitz, T.A.

(1995) Cell 82: 193-207

Released	1996-04-03
Method	X-RAY DIFFRACTION 3 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (GAMMA DELTA RESOLVASE) (protein) SITE I OF RES DNA (nucleic acid)

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1GPC \| pdb_00001gpc	Download File View File

CORE GP32, DNA-BINDING PROTEIN

Shamoo, Y., Friedman, A.M., Parsons, M.R., Konigsberg, W.H., Steitz, T.A.

(1995) Nature 376: 362-366

Released	1995-10-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Tequatrovirus T4
Macromolecule	PROTEIN (CORE GP32) (protein)
Unique Ligands	ZN

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1HCR \| pdb_00001hcr	Download File View File

HIN RECOMBINASE BOUND TO DNA: THE ORIGIN OF SPECIFICITY IN MAJOR AND MINOR GROOVE INTERACTIONS

Feng, J.-A., Johnson, R.C., Dickerson, R.E.

(1994) Science 263: 348-355

Released	1994-04-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Macromolecule	PROTEIN (HIN RECOMBINASE) (protein) DNA (5'-D(TPCPTPTPAPTPCPAPAPAPAPAPC)-3') (nucleic acid) DNA (5'-D(TPGPTPTPTPTPTPGPAPTPAPAPGP*A)-3') (nucleic acid)

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1HLV \| pdb_00001hlv	Download File View File

CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA

Tanaka, Y., Nureki, O., Kurumizaka, H., Fukai, S., Kawaguchi, S., Ikuta, M., Iwahara, J., Okazaki, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) EMBO J 20: 6612-6618

Released	2002-01-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	MAJOR CENTROMERE AUTOANTIGEN B (protein) CENP-B BOX DNA (nucleic acid)

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1HRY \| pdb_00001hry	Download File View File

THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTID-DIMENSIONAL HETERONUCLEAR-EDITED AND-FILTERED NMR

Clore, G.M., Werner, M.H., Huth, J.R., Gronenborn, A.M.

(1995) Cell 81: 704-705

Released	1995-09-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HUMAN SRY (protein) DNA (5'-D(GPCPAPCPAPAPAPC)-3') (nucleic acid) DNA (5'-D(GPTPTPTPGPTPGPC)-3') (nucleic acid)

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1HRZ \| pdb_00001hrz	Download File View File

THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND-FILTERED NMR

Clore, G.M., Werner, M.H., Huth, J.R., Gronenborn, A.M.

(1995) Cell 81: 704-705

Released	1995-09-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HUMAN SRY (protein) DNA (5'-D(GPCPAPCPAPAPAPC)-3') (nucleic acid) DNA (5'-D(GPTPTPTPGPTPGPC)-3') (nucleic acid)

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1IGN \| pdb_00001ign	Download File View File

DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE

Koenig, P., Giraldo, R., Chapman, L., Rhodes, D.

(1996) Cell 85: 125-136

Released	1997-01-27
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROTEIN (RAP1) (protein) DNA (5'-D(CPCPGPCPAPCPAPCPCPCPAPCPAPCPAPCPC PAPG)-3') (nucleic acid) DNA (5'-D(CPCPTPGPGPTPGPTPGPTPGPGPGPTPGPTPG PCPG)-3') (nucleic acid)

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1IJW \| pdb_00001ijw	Download File View File

Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.

Chiu, T.K., Sohn, C., Johnson, R.C., Dickerson, R.E.

(2002) EMBO J 21: 801-814

Released	2002-02-22
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Macromolecule	DNA-INVERTASE HIN (protein) 5'-D(APTP(CBR)PTPTPAPTPCPAPAPAPAPAPC)-3' (nucleic acid) 5'-D(TPGPTPTPTPTPTPGPAPTPAPAPGPA)-3' (nucleic acid)
Unique Ligands	TRS

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1IV6 \| pdb_00001iv6	Download File View File

Solution Structure of the DNA Complex of Human TRF1

Nishikawa, T., Okamura, H., Nagadoi, A., Konig, P., Rhodes, D., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Structure 9: 1237-1251

Released	2002-04-17
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TELOMERIC REPEAT BINDING FACTOR 1 (protein) 5'-D(CPCPCPTPAPAPCPCPCPTPAPAPC)-3' (nucleic acid) 5'-D(GPTPTPAPGPGPGPTPTPAPGPGPG)-3' (nucleic acid)

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1J5N \| pdb_00001j5n	Download File View File

Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA

Masse, J.E., Wong, B., Yen, Y.-M., Allain, F.H.-T., Johnson, R.C., Feigon, J.

(2002) J Mol Biology 323: 263-284

Released	2002-10-16
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Nonhistone chromosomal protein 6A (protein) 5'-D(CPTPGPAPAPCPAPAPTPCPAPCPCPCPC)-3' (nucleic acid) 5'-D(GPGPGPGPTPGPAPTPTPGPTPTPCPAPG)-3' (nucleic acid)

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1J9N \| pdb_00001j9n	Download File View File

Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3dGCATCG)-ALA]-[p5dCGTAGC]

Gomez-Pinto, I., Marchan, V., Gago, F., Grandas, A., Gonzalez, C.

(2003) Chembiochem 4: 40-49

Released	2003-01-21
Method	SOLUTION NMR
Macromolecule	peptide ACE-LYS-TRP-LYS-HSE-ALA (protein) 5'-D(CPGPTPAPGPC)-3' (nucleic acid) 5'-D(GPCPTPAPCP(PGN))-3' (nucleic acid)

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1JB7 \| pdb_00001jb7	Download File View File

DNA G-Quartets in a 1.86 A Resolution Structure of an Oxytricha nova Telomeric Protein-DNA Complex

Horvath, M.P., Schultz, S.C.

(2001) J Mol Biology 310: 367-377

Released	2001-06-11
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Sterkiella nova
Macromolecule	telomere-binding protein alpha subunit (protein) telomere-binding protein beta subunit (protein) 5'-D(GPGPGPGPTPTPTPTPGPGPGPG)-3' (nucleic acid)
Unique Ligands	CL, NA

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1JEY \| pdb_00001jey	Download File View File

Crystal Structure of the Ku heterodimer bound to DNA

Walker, J.R., Corpina, R.A., Goldberg, J.

(2001) Nature 412: 607-614

Released	2001-08-10
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Ku70 (protein) Ku80 (protein) DNA (34-MER) (nucleic acid) DNA (5'-D(GPTPTPTPTPTPAPGPTPTPTPAPTPTPGPGPGPCPGPCP*G)-3') (nucleic acid)

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1JJ6 \| pdb_00001jj6	Download File View File

Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.

Chiu, T.K., Sohn, C., Johnson, R.C., Dickerson, R.E.

(2002) EMBO J 21: 801-814

Released	2002-02-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Macromolecule	DNA-INVERTASE HIN (protein) 5'-D(APTPCPTPTPAPTPCPAPAPAPAPAPC)-3' (nucleic acid) 5'-D(TPGPTP(5IT)PTPTPTPGPAPTPAPAPGPA)-3' (nucleic acid)
Unique Ligands	TRS

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1JJ8 \| pdb_00001jj8	Download File View File

Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations

Chiu, T.K., Sohn, C., Johnson, R.C., Dickerson, R.E.

(2002) EMBO J 21: 801-814

Released	2002-02-22
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Macromolecule	DNA-INVERTASE HIN (protein) 5'-D(APTPCPTPTPAPTPCPAPAPAPAPAPC)-3' (nucleic acid) 5'-D(TPGP(5IT)PTPTPTPTPGPAPTPAPAPGPA)-3' (nucleic acid)

1 to 25 of 1,235 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

Symmetry Type

SCOP Classification

1AHD | pdb_00001ahd

1AKH | pdb_00001akh

1AOI | pdb_00001aoi

1APL | pdb_00001apl

1AZP | pdb_00001azp

1AZQ | pdb_00001azq

1BBX | pdb_00001bbx

1BF4 | pdb_00001bf4

1BNZ | pdb_00001bnz

1C8C | pdb_00001c8c

1GDT | pdb_00001gdt

1GPC | pdb_00001gpc

1HCR | pdb_00001hcr

1HLV | pdb_00001hlv

1HRY | pdb_00001hry

1HRZ | pdb_00001hrz

1IGN | pdb_00001ign

1IJW | pdb_00001ijw

1IV6 | pdb_00001iv6

1J5N | pdb_00001j5n

1J9N | pdb_00001j9n

1JB7 | pdb_00001jb7

1JEY | pdb_00001jey

1JJ6 | pdb_00001jj6

1JJ8 | pdb_00001jj8