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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "DNA BINDING"

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Search Summary

This query matches 4,864 Structures.

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Structure Determination Methodology

experimental (4,864)

Scientific Name of Source Organism

	Homo sapiens (1,699)
	synthetic construct (830)
	Escherichia coli (306)
	Escherichia coli K-12 (178)
	Mus musculus (170)
	Saccharomyces cerevisiae (131)
	Saccharomyces cerevisiae S288C (110)
	Xenopus laevis (102)
	Arabidopsis thaliana (87)
	Mycobacterium tuberculosis H37Rv (58)

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Taxonomy

	Eukaryota (2,501)
	Bacteria (1,858)
	other sequences (850)
	Archaea (315)
	Duplodnaviria (114)
	Monodnaviria (65)
	Riboviria (39)
	unclassified sequences (39)
	Varidnaviria (35)
	Eukaryota (eukaryotes) (21)

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Experimental Method

	X-RAY DIFFRACTION (3,612)
	ELECTRON MICROSCOPY (793)
	SOLUTION NMR (458)
	SOLID-STATE NMR (2)
	SOLUTION SCATTERING (1)

Polymer Entity Type

	Protein (4,860)
	DNA (1,924)
	RNA (106)
	NA-hybrid (11)

Refinement Resolution (Å)

	0.5 - 1.0 (5)
	1.0 - 1.5 (188)
	1.5 - 2.0 (1,043)
	2.0 - 2.5 (1,103)
	2.5 - 3.0 (973)
	3.0 - 3.5 (604)
	3.5 - 4.0 (246)
	4.0 - 4.5 (116)
	> 4.5 (127)

Release Date

	1985 - 1989 (4)
	1990 - 1994 (29)
	1995 - 1999 (141)
	2000 - 2004 (263)
	2005 - 2009 (416)
	2010 - 2014 (620)
	2015 - 2019 (1,316)
	2020 - 2024 (1,934)
	2025 - 2029 (141)

Enzyme Classification Name

	Hydrolases (743)
	Transferases (452)
	Lyases (192)
	Isomerases (125)
	Oxidoreductases (52)
	Ligases (37)

Symmetry Type

	Asymmetric (2,957)
	Cyclic (1,739)
	Dihedral (178)
	Helical (64)
	Tetrahedral (46)
	Octahedral (5)
	Icosahedral (1)

SCOP Classification

	All alpha proteins (920)
	Artifacts (472)
	Alpha and beta proteins (a+b) (214)
	All beta proteins (248)
	Alpha and beta proteins (a/b) (139)
	Small proteins (61)
	Coiled coil proteins (9)
	Multi-domain proteins (alpha and beta) (13)
	Peptides (15)
	Low resolution protein structures (1)

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AllSelected

1 to 25 of 4,864 Structures

Page 1 of 195

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1AAB \| pdb_00001aab	Download File View File

NMR STRUCTURE OF RAT HMG1 HMGA FRAGMENT

Hardman, C.H., Broadhurst, R.W., Raine, A.R.C., Grasser, K.D., Thomas, J.O., Laue, E.D.

(1995) Biochemistry 34: 16596-16607

Released	1996-03-08
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	HIGH MOBILITY GROUP PROTEIN (protein)

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1E3M \| pdb_00001e3m	Download File View File

The crystal structure of E. coli MutS binding to DNA with a G:T mismatch

Lamers, M.H., Perrakis, A., Enzlin, J.H., Winterwerp, H.H.K., De Wind, N., Sixma, T.K.

(2000) Nature 407: 711

Released	2000-11-01
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTS (protein) 5'-D(APGPCPTPGPCPCPAPGPGPCPAPCPCPAP GPTPGPTPCPAPGPCPGPTPCPCPTPAPT)-3' (nucleic acid) 5'-D(APTPAPGPGPAPCPGPCPTPGPAPCPAPCP TPGPGPTPGPCPTPTPGPGPCPAPGPCPT)-3' (nucleic acid)
Unique Ligands	ADP, MG

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1FTZ \| pdb_00001ftz	Download File View File

NUCLEAR MAGNETIC RESONANCE SOLUTION STRUCTURE OF THE FUSHI TARAZU HOMEODOMAIN FROM DROSOPHILA AND COMPARISON WITH THE ANTENNAPEDIA HOMEODOMAIN

Qian, Y.Q., Furukubo-Tokunaga, K., Resendez-Perez, D., Muller, M., Gehring, W.J., Wuthrich, K.

(1994) J Mol Biology 238: 333-345

Released	1994-05-31
Method	SOLUTION NMR
Organisms	Drosophila melanogaster
Macromolecule	FUSHI TARAZU PROTEIN (protein)

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1H0X \| pdb_00001h0x	Download File View File

Structure of Alba: an archaeal chromatin protein modulated by acetylation

Wardleworth, B.N., Russell, R.J.M., Bell, S.D., Taylor, G.L., White, M.F.

(2002) EMBO J 21: 4654

Released	2002-09-05
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA BINDING PROTEIN SSO10B (protein)

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1H0Y \| pdb_00001h0y	Download File View File

Structure of Alba: an archaeal chromatin protein modulated by acetylation

Wardleworth, B.N., Russell, R.J.M., Bell, S.D., Taylor, G.L., White, M.F.

(2002) EMBO J 21: 4654

Released	2002-09-05
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA BINDING PROTEIN SSO10B (protein)
Unique Ligands	SO4

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1H1J \| pdb_00001h1j	Download File View File

The SAP domain is a DNA-Binding Domain Capable of Binding S/MAR DNA

Jacobsen, J.O.B., Freund, S.M.V., Bycroft, M.

To be published

Released	2002-08-08
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	THO1 PROTEIN (protein)

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1HMA \| pdb_00001hma	Download File View File

THE SOLUTION STRUCTURE AND DYNAMICS OF THE DNA BINDING DOMAIN OF HMG-D FROM DROSOPHILA MELANOGASTER

Jones, D.N.M., Searles, M.A., Shaw, G.L., Churchill, M.E.A., Ner, S.S., Keeler, J., Travers, A.A., Neuhaus, D.

(1994) Structure 2: 609-627

Released	1994-07-31
Method	SOLUTION NMR
Organisms	Drosophila melanogaster
Macromolecule	HMG-D (protein)

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1HME \| pdb_00001hme	Download File View File

STRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1

Weir, H.M., Kraulis, P.J., Hill, C.S., Raine, A.R.C., Laue, E.D., Thomas, J.O.

(1993) EMBO J 12: 1311-1319

Released	1994-05-31
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	HIGH MOBILITY GROUP PROTEIN FRAGMENT-B (protein)

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1HMF \| pdb_00001hmf	Download File View File

STRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1

Weir, H.M., Kraulis, P.J., Hill, C.S., Raine, A.R.C., Laue, E.D., Thomas, J.O.

(1993) EMBO J 12: 1311-1319

Released	1994-05-31
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	HIGH MOBILITY GROUP PROTEIN FRAGMENT-B (protein)

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1HSM \| pdb_00001hsm	Download File View File

THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA

Read, C.M., Cary, P.D., Crane-Robinson, C., Driscoll, P.C., Carillo, M.O.M., Norman, D.G.

To be published

Released	1995-02-07
Method	SOLUTION NMR
Organisms	Cricetulus griseus
Macromolecule	HIGH MOBILITY GROUP PROTEIN 1 (protein)
Unique Ligands	BME

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1HSN \| pdb_00001hsn	Download File View File

THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA

Read, C.M., Cary, P.D., Crane-Robinson, C., Driscoll, P.C., Carillo, M.O.M., Norman, D.G.

To be published

Released	1995-02-07
Method	SOLUTION NMR
Organisms	Cricetulus griseus
Macromolecule	HIGH MOBILITY GROUP PROTEIN 1 (protein)
Unique Ligands	BME

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1HUE \| pdb_00001hue	Download File View File

HISTONE-LIKE PROTEIN

Vis, H., Mariani, M., Vorgias, C.E., Wilson, K.S., Kaptein, R., Boelens, R.

(1995) J Mol Biology 254: 692-703

Released	1995-10-15
Method	SOLUTION NMR
Organisms	Geobacillus stearothermophilus
Macromolecule	HU PROTEIN (protein)

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1NHM \| pdb_00001nhm	Download File View File

THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA

Read, C.M., Cary, P.D., Crane-Robinson, C., Driscoll, P.C., Carillo, M.O.M., Norman, D.G.

(1995) Nucleic Acids Mol Biol 9: 222

Released	1995-02-07
Method	SOLUTION NMR
Organisms	Cricetulus griseus
Macromolecule	HIGH MOBILITY GROUP PROTEIN 1 (protein)

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1NHN \| pdb_00001nhn	Download File View File

THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA

Read, C.M., Cary, P.D., Crane-Robinson, C., Driscoll, P.C., Carillo, M.O.M., Norman, D.G.

(1995) Nucleic Acids Mol Biol 9: 222

Released	1995-02-07
Method	SOLUTION NMR
Organisms	Cricetulus griseus
Macromolecule	HIGH MOBILITY GROUP PROTEIN 1 (protein)

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1OH5 \| pdb_00001oh5	Download File View File

THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A C:A MISMATCH

Natrajan, G., Lamers, M.H., Enzlin, J.H., Winterwerp, H.H.K., Perrakis, A., Sixma, T.K.

(2003) Nucleic Acids Res 31: 4814

Released	2003-08-08
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTS (protein) 5'-D(APGPCPTPGPCPCPAPCPGP CPAPCPCPAPGPTPGPTPCPAPGPCPGPTP CPCPTPAPT)-3' (nucleic acid) 5'-D(APTPAPGPGPAPCPGPCPTP GPAPCPAPCPTPGPGPTPGPCPAPTPGPGP CPAPGPCPT)-3' (nucleic acid)
Unique Ligands	ADP, MG

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1OH6 \| pdb_00001oh6	Download File View File

THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH AN A:A MISMATCH

Natrajan, G., Lamers, M.H., Enzlin, J.H., Winterwerp, H.H.K., Perrakis, A., Sixma, T.K.

(2003) Nucleic Acids Res 31: 4814

Released	2003-08-08
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTS (protein) 5'-D(APGPCPTPGPCPCPAPAPGP CPAPCPCPAPGPTPGPTPCPAPGPCPGPTP CPCPTPAPT)-3' (nucleic acid) 5'-D(APTPAPGPGPAPCPGPCPTP GPAPCPAPCPTPGPGPTPGPCPAPTPGPGP CPAPGPCPT)-3' (nucleic acid)
Unique Ligands	ADP, MG

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1OH7 \| pdb_00001oh7	Download File View File

THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A G:G MISMATCH

Natrajan, G., Lamers, M.H., Enzlin, J.H., Winterwerp, H.H.K., Perrakis, A., Sixma, T.K.

(2003) Nucleic Acids Res 31: 4814

Released	2003-08-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTS (protein) 5'-D(APGPCPTPGPCPCPAPGPGP CPAPCPCPAPGPTPGPTPCPAPGPCPGPTP CPCPTPAPT)-3' (nucleic acid) 5'-D(APTPAPGPGPAPCPGPCPTP GPAPCPAPCPTPGPGPTPGPCPGPTPGPGP CPAPGPCPT)-3' (nucleic acid)
Unique Ligands	ADP, MG

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1OH8 \| pdb_00001oh8	Download File View File

THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH AN UNPAIRED THYMIDINE

Natrajan, G., Lamers, M.H., Enzlin, J.H., Winterwerp, H.H.K., Perrakis, A., Sixma, T.K.

(2003) Nucleic Acids Res 31: 4814

Released	2003-08-08
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTS (protein) 5'-D(APGPCPTPGPCPCPAPGPGP CPAPCPCPAPGPTPGPTPCPAPGPCPGPTPCPCP TPAPT)-3' (nucleic acid) 5'-D(APTPAPGPGPAPCPGPCPTP GPAPCPAPCPTPGPGPTPGPCPCPTPTPGPGPCP APGPCP*T)-3' (nucleic acid)
Unique Ligands	ADP, MG

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1PES \| pdb_00001pes	Download File View File

NMR SOLUTION STRUCTURE OF THE TETRAMERIC MINIMUM TRANSFORMING DOMAIN OF P53

Lee, W., Harvey, T.S., Yin, Y., Yau, P., Litchfield, D., Arrowsmith, C.H.

(1994) Nat Struct Biol 1: 877-890

Released	1995-02-07
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TUMOR SUPPRESSOR P53 (protein)

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1PET \| pdb_00001pet	Download File View File

NMR SOLUTION STRUCTURE OF THE TETRAMERIC MINIMUM TRANSFORMING DOMAIN OF P53

Lee, W., Harvey, T.S., Yin, Y., Yau, P., Litchfield, D., Arrowsmith, C.H.

(1994) Nat Struct Biol 1: 877-890

Released	1995-02-07
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TUMOR SUPPRESSOR P53 (protein)

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1PLQ \| pdb_00001plq	Download File View File

CRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY FACTOR PCNA

Krishna, T.S.R., Kong, X.-P., Gary, S., Burgers, P.M., Kuriyan, J.

(1994) Cell 79: 1233-1243

Released	1995-03-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) (protein)
Unique Ligands	HG

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1PLR \| pdb_00001plr	Download File View File

CRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY FACTOR PCNA

Krishna, T.S.R., Kong, X.-P., Gary, S., Burgers, P.M., Kuriyan, J.

(1994) Cell 79: 1233-1243

Released	1995-03-31
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) (protein)

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1V1Q \| pdb_00001v1q	Download File View File

Crystal structure of PriB- a primosomal DNA replication protein of Escherichia coli

Liu, J.-H., Chang, T.-W., Huang, C.-Y., Chang, M.-C., Chen, S.-U., Wu, H.-N., Hsiao, C.-D.

(2004) J Biological Chem 279: 50465

Released	2004-10-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli K-12
Macromolecule	PRIMOSOMAL REPLICATION PROTEIN N (protein)
Unique Ligands	CYS

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1VCC \| pdb_00001vcc	Download File View File

AMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I RESIDUES 1-77, EXPERIMENTAL ELECTRON DENSITY FOR RESIDUES 1-77

Sharma, A., Hanai, R., Mondragon, A.

(1994) Structure 2: 767-777

Released	1996-03-08
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Vaccinia virus WR
Macromolecule	DNA TOPOISOMERASE I (protein)

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1W7A \| pdb_00001w7a	Download File View File

ATP bound MutS

Lamers, M.H., Georgijevic, D., Lebbink, J., Winterwerp, H.H.K., Agianian, B., de Wind, N., Sixma, T.K.

(2004) J Biological Chem 279: 43879

Released	2004-09-10
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Escherichia coli
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTS (protein) 5'-D(APGPCPTPGPCPCPAPGPGP CPAPCPCPAPGPTPGPTPCPAPGPCPGPTPCPCPTP* APT)-3' (nucleic acid) 5'-D(APTPAPGPGPAPCPGPCPTP GPAPCPAPCPTPGPGPTPGPCPTPTPGPGPCPAPGP CP*T)-3' (nucleic acid)
Unique Ligands	ATP, MG

1 to 25 of 4,864 Structures

Page 1 of 195

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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

1AAB | pdb_00001aab

1E3M | pdb_00001e3m

1FTZ | pdb_00001ftz

1H0X | pdb_00001h0x

1H0Y | pdb_00001h0y

1H1J | pdb_00001h1j

1HMA | pdb_00001hma

1HME | pdb_00001hme

1HMF | pdb_00001hmf

1HSM | pdb_00001hsm

1HSN | pdb_00001hsn

1HUE | pdb_00001hue

1NHM | pdb_00001nhm

1NHN | pdb_00001nhn

1OH5 | pdb_00001oh5

1OH6 | pdb_00001oh6

1OH7 | pdb_00001oh7

1OH8 | pdb_00001oh8

1PES | pdb_00001pes

1PET | pdb_00001pet

1PLQ | pdb_00001plq

1PLR | pdb_00001plr

1V1Q | pdb_00001v1q

1VCC | pdb_00001vcc

1W7A | pdb_00001w7a