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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Williams, J.S."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Homo sapiens (6)
	Pyrococcus furiosus (6)
	Saccharomyces cerevisiae (4)
	Schizosaccharomyces pombe (4)
	Schizosaccharomyces pombe 972h- (2)
	synthetic construct (1)

Taxonomy

	Eukaryota (14)
	Archaea (6)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (20)

Polymer Entity Type

	Protein (20)
	DNA (10)
	NA-hybrid (3)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (6)
	2.0 - 2.5 (6)
	2.5 - 3.0 (5)
	3.0 - 3.5 (2)

Release Date

	2005 - 2009 (4)
	2010 - 2014 (11)
	2015 - 2019 (1)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (15)
	Ligases (2)

Symmetry Type

	Asymmetric (15)
	Cyclic (5)
	Dihedral (1)

SCOP Classification

Alpha and beta proteins (a+b) (2)

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1 to 20 of 20 Structures

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3DSC \| pdb_00003dsc	Download File View File

Crystal structure of P. furiosus Mre11 DNA synaptic complex

Williams, R.S., Moncalian, G., Shin, D.S., Tainer, J.A.

(2008) Cell 135: 97-109

Released	2008-10-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pyrococcus furiosus
Macromolecule	DNA double-strand break repair protein mre11 (protein) DNA (5'-D(PDCPDAPDCPDAPDAPDGPDCPDTPDTPDTPDTPDGPDCPDTPDTPDGPDTPDGPDAPDC)-3') (nucleic acid)

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3DSD \| pdb_00003dsd	Download File View File

Crystal structure of P. furiosus Mre11-H85S bound to a branched DNA and manganese

Williams, R.S., Moiani, D., Tainer, J.A.

(2008) Cell 135: 97-109

Released	2008-10-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus furiosus
Macromolecule	DNA double-strand break repair protein mre11 (protein) DNA (5'-D(DCPDGPDCPDGPDCPDAPDCPDAPDAPDGPDCPDTPDTPDTPDTPDGPDCPDTPDTPDGPDTPDGPDGPDAPDTPDA)-3') (nucleic acid)
Unique Ligands	MN

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3HUE \| pdb_00003hue	Download File View File

Structure of the S. pombe Nbs1 FHA-BRCT1-BRCT2 domains

Williams, R.S., Guenther, G., Tainer, J.A.

(2009) Cell 139: 87-99

Released	2009-10-13
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	DNA repair and telomere maintenance protein nbs1 (protein)

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3HUF \| pdb_00003huf	Download File View File

Structure of the S. pombe Nbs1-Ctp1 complex

Williams, R.S., Guenther, G., Tainer, J.A.

(2009) Cell 139: 87-99

Released	2009-10-13
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	DNA repair and telomere maintenance protein nbs1 (protein) Double-strand break repair protein ctp1 (protein)
Unique Ligands	SCN

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3L40 \| pdb_00003l40	Download File View File

Crystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains

Williams, R.S., Williams, J.S., Guenther, G., Tainer, J.A.

(2010) EMBO J 29: 1136-1148

Released	2010-02-09
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	BRCT-containing protein 1 (protein)

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3L41 \| pdb_00003l41	Download File View File

Crystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains in complex with phosphorylated H2A

Williams, R.S., Williams, J.S., Guenther, G., Tainer, J.A.

(2010) EMBO J 29: 1136-1148

Released	2010-02-09
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	BRCT-containing protein 1 (protein) phosphorylated H2A tail (protein)

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3QKR \| pdb_00003qkr	Download File View File

Mre11 Rad50 binding domain bound to Rad50

Williams, G.J., Williams, R.S., Arvai, A., Moncalian, G., Tainer, J.A.

(2011) Nat Struct Mol Biol 18: 423-431

Released	2011-03-30
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Pyrococcus furiosus
Macromolecule	DNA double-strand break repair protein mre11 (protein) DNA double-strand break repair rad50 ATPase (protein)
Unique Ligands	PO4

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3QKS \| pdb_00003qks	Download File View File

Mre11 Rad50 binding domain bound to Rad50

Williams, G.J., Williams, R.S., Arvai, A., Moncalian, G., Tainer, J.A.

(2011) Nat Struct Mol Biol 18: 423-431

Released	2011-03-30
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pyrococcus furiosus
Macromolecule	DNA double-strand break repair protein mre11 (protein) DNA double-strand break repair rad50 ATPase (protein)

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3QKT \| pdb_00003qkt	Download File View File

Rad50 ABC-ATPase with adjacent coiled-coil region in complex with AMP-PNP

Williams, G.J., Williams, R.S., Arvai, A., Moncalian, G., Tainer, J.A.

(2011) Nat Struct Mol Biol 18: 423-431

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pyrococcus furiosus
Macromolecule	DNA double-strand break repair rad50 ATPase (protein)
Unique Ligands	ANP, MG

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3QKU \| pdb_00003qku	Download File View File

Mre11 Rad50 binding domain in complex with Rad50 and AMP-PNP

Williams, G.J., Williams, R.S., Arvai, A., Moncalian, G., Tainer, J.A.

(2011) Nat Struct Mol Biol 18: 423-431

Released	2011-03-30
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Pyrococcus furiosus
Macromolecule	DNA double-strand break repair protein mre11 (protein) DNA double-strand break repair rad50 ATPase (protein)
Unique Ligands	ANP, MG

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3SZQ \| pdb_00003szq	Download File View File

Structure of an S. pombe APTX/DNA/AMP/Zn complex

Tumbale, P., Krahn, J., Williams, R.S.

(2011) Nat Struct Mol Biol 18: 1189-1195

Released	2011-10-12
Method	X-RAY DIFFRACTION 2.353 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Aprataxin-like protein (protein) 5'-D(CPCPCPTPG)-3' (nucleic acid) 5'-D(TPAPTPCPGPGPAPAPTPCPAPGPGP*G)-3' (nucleic acid)
Unique Ligands	AMP, BME, ZN

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4NDF \| pdb_00004ndf	Download File View File

Human Aprataxin (Aptx) bound to RNA-DNA, AMP, and Zn - product complex

Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

(2013) Nature 506: 111-115

Released	2013-12-18
Method	X-RAY DIFFRACTION 1.944 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) 5'-D(GPAPAPTPCPAPTPAPAPC)-3' (nucleic acid) 5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3' (hybrid)
Unique Ligands	AMP, BME, K, NA, ZN

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4NDG \| pdb_00004ndg	Download File View File

Human Aprataxin (Aptx) bound to RNA-DNA and Zn - adenosine vanadate transition state mimic complex

Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

(2013) Nature 506: 111-115

Released	2013-12-18
Method	X-RAY DIFFRACTION 2.541 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) 5'-D(GPAPAPTPCPAPTPAPAPC)-3' (nucleic acid) 5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3' (hybrid)
Unique Ligands	V5A, ZN

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4NDH \| pdb_00004ndh	Download File View File

Human Aprataxin (Aptx) bound to DNA, AMP, and Zn - product complex

Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

(2013) Nature 506: 111-115

Released	2013-12-18
Method	X-RAY DIFFRACTION 1.848 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) 5'-D(PGPTPTPCPTPAPGPAPAPC)-3' (nucleic acid)
Unique Ligands	AMP, ZN

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4NDI \| pdb_00004ndi	Download File View File

Human Aprataxin (Aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and Zn - product complex

Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

(2013) Nature 506: 111-115

Released	2013-12-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Aprataxin (protein) 5'-D(GPAPAPTPCPAPTPAPAPC)-3' (nucleic acid) 5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3' (hybrid)
Unique Ligands	AMP, BME, GOL, K, NA, ZN

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4X01 \| pdb_00004x01	Download File View File

S. pombe Ctp1 tetramerization domain

Andres, S.N., Williams, R.S.

(2015) Nat Struct Mol Biol 22: 158-166

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.201 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	DNA binding ctp1 (protein)
Unique Ligands	EDO

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7KR3 \| pdb_00007kr3	Download File View File

Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate

Tumbale, P.P., Williams, R.S.

(2021) Nat Commun 12: 482-482

Released	2021-02-03
Method	X-RAY DIFFRACTION 2.778 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	DNA ligase 1 (protein) DNA (5'-D(APAPTPGPTPCPTPGPCPCPCPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPAPAPTPGPGPGPCPAPGPAPCPAPTPT)-3') (nucleic acid) DNA (5'-D(PAPTPTPCPTPGP*C)-3') (nucleic acid)
Unique Ligands	ACT, AMP

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7KR4 \| pdb_00007kr4	Download File View File

Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex

Tumbale, P.P., Williams, R.S.

(2021) Nat Commun 12: 482-482

Released	2021-02-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	DNA ligase 1 (protein) DNA (5'-D(APAPTPGPTPCPTPGPCPCPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPAPAPTPGPGPGPCPAPGPAPCPAPTPT)-3') (nucleic acid) DNA (5'-D(PAPTPTPCPTPGPC)-3') (nucleic acid)
Unique Ligands	ACT, AMP

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7N3Y \| pdb_00007n3y	Download File View File

Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA

Wojtaszek, J.L., Krahn, J., Wallace, B.D., Williams, R.S.

(2022) Cell Rep 41: 111448-111448

Released	2022-09-28
Method	X-RAY DIFFRACTION 2.73 Å
Organisms	Saccharomyces cerevisiae synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) endonuclease 2 (protein) DNA (5'-D(CPCPGPAPAPAPTPTP(PST)P(SC)P(GS)P(GS)P(AS))-3') (nucleic acid) DNA (5'-D(TPCPCPGPAPAPAPTP(PST)P(PST)P(SC)P(GS)P(GS))-3') (nucleic acid)
Unique Ligands	CA, CIT, EDO, TAR, TLA

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7N3Z \| pdb_00007n3z	Download File View File

Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain

Wojtaszek, J.L., Wallace, B.D., Williams, R.S.

(2022) Cell Rep 41: 111448-111448

Released	2022-09-28
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA-(apurinic or apyrimidinic site) endonuclease 2 (protein)
Unique Ligands	CL, EDO, MG

1 to 20 of 20 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.

3DSC | pdb_00003dsc

Crystal structure of P. furiosus Mre11 DNA synaptic complex

3DSD | pdb_00003dsd

Crystal structure of P. furiosus Mre11-H85S bound to a branched DNA and manganese

3HUE | pdb_00003hue

Structure of the S. pombe Nbs1 FHA-BRCT1-BRCT2 domains

3HUF | pdb_00003huf

Structure of the S. pombe Nbs1-Ctp1 complex

3L40 | pdb_00003l40

Crystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains

3L41 | pdb_00003l41

Crystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains in complex with phosphorylated H2A

3QKR | pdb_00003qkr

Mre11 Rad50 binding domain bound to Rad50

3QKS | pdb_00003qks

Mre11 Rad50 binding domain bound to Rad50

3QKT | pdb_00003qkt

Rad50 ABC-ATPase with adjacent coiled-coil region in complex with AMP-PNP

3QKU | pdb_00003qku

Mre11 Rad50 binding domain in complex with Rad50 and AMP-PNP

3SZQ | pdb_00003szq

Structure of an S. pombe APTX/DNA/AMP/Zn complex

4NDF | pdb_00004ndf

Human Aprataxin (Aptx) bound to RNA-DNA, AMP, and Zn - product complex

4NDG | pdb_00004ndg

Human Aprataxin (Aptx) bound to RNA-DNA and Zn - adenosine vanadate transition state mimic complex

4NDH | pdb_00004ndh

Human Aprataxin (Aptx) bound to DNA, AMP, and Zn - product complex

4NDI | pdb_00004ndi

Human Aprataxin (Aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and Zn - product complex

4X01 | pdb_00004x01

S. pombe Ctp1 tetramerization domain

7KR3 | pdb_00007kr3

Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate

7KR4 | pdb_00007kr4

Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex

7N3Y | pdb_00007n3y

Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA

7N3Z | pdb_00007n3z

Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain

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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

3DSC | pdb_00003dsc

3DSD | pdb_00003dsd

3HUE | pdb_00003hue

3HUF | pdb_00003huf

3L40 | pdb_00003l40

3L41 | pdb_00003l41

3QKR | pdb_00003qkr

3QKS | pdb_00003qks

3QKT | pdb_00003qkt

3QKU | pdb_00003qku

3SZQ | pdb_00003szq

4NDF | pdb_00004ndf

4NDG | pdb_00004ndg

4NDH | pdb_00004ndh

4NDI | pdb_00004ndi

4X01 | pdb_00004x01

7KR3 | pdb_00007kr3

7KR4 | pdb_00007kr4

7N3Y | pdb_00007n3y

7N3Z | pdb_00007n3z