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PDB: 23 results
5CL8
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BU of 5cl8 by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 144 hours)
Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.38 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5CL7
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BU of 5cl7 by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (18% substrate/82% product at 96 hours)
Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.44 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
3JXY
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BU of 3jxy by Molmil
Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing a GT Mismatch
Descriptor: DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*CP*TP*GP*AP*CP*GP*GP*G)-3'), alkylpurine DNA glycosylase AlkD
Authors:Rubinson, E.H, Eichman, B.F.
Deposit date:2009-09-21
Release date:2010-09-22
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:An unprecedented nucleic acid capture mechanism for excision of DNA damage.
Nature, 468, 2010
5CL9
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BU of 5cl9 by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 240 hours)
Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.538 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5CLD
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BU of 5cld by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing an oxocarbenium-intermediate analog and a free 3-methyladenine nucleobase
Descriptor: 3-METHYL-3H-PURIN-6-YLAMINE, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.541 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5CLA
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BU of 5cla by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 360 hours)
Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.541 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5CL6
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BU of 5cl6 by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (33% substrate/67% product at 72 hours)
Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.541 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5CL5
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BU of 5cl5 by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (51% substrate/49% product at 48 hours)
Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.569 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5UUH
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BU of 5uuh by Molmil
Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing a fluorinated abasic site (9-mer product complex)
Descriptor: CALCIUM ION, DNA (5'-D(*AP*GP*GP*CP*AP*(ORF)P*AP*GP*C)-3'), DNA (5'-D(*TP*GP*CP*TP*TP*TP*GP*CP*C)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2017-02-16
Release date:2017-07-19
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.569 Å)
Cite:Toxicity and repair of DNA adducts produced by the natural product yatakemycin.
Nat. Chem. Biol., 13, 2017
3JX7
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BU of 3jx7 by Molmil
Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-METHYLADENINE analog
Descriptor: DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3'), alkylpurine DNA glycosylase AlkD
Authors:Rubinson, E.H, Eichman, B.F.
Deposit date:2009-09-18
Release date:2010-09-22
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:An unprecedented nucleic acid capture mechanism for excision of DNA damage.
Nature, 468, 2010
5UUF
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BU of 5uuf by Molmil
Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (12-mer product complex)
Descriptor: DNA (5'-D(*CP*CP*CP*CP*AP*(ORP)P*AP*GP*CP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*GP*CP*TP*TP*TP*GP*GP*GP*G)-3'), DNA-7-methylguanine glycosylase, ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2017-02-16
Release date:2017-07-19
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.612 Å)
Cite:Toxicity and repair of DNA adducts produced by the natural product yatakemycin.
Nat. Chem. Biol., 13, 2017
7LXH
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BU of 7lxh by Molmil
Bacillus cereus DNA glycosylase AlkD bound to a CC1065-adenine nucleobase adduct and DNA containing an abasic site
Descriptor: 7-{7-[(1R)-1-{[(4P)-6-amino-3H-purin-3-yl]methyl}-5-hydroxy-8-methyl-1,6-dihydropyrrolo[3,2-e]indole-3(2H)-carbonyl]-4-hydroxy-5-methoxy-1,6-dihydropyrrolo[3,2-e]indole-3(2H)-carbonyl}-4-hydroxy-5-methoxy-1,6-dihydropyrrolo[3,2-e]indole-3(2H)-carboxamide, CALCIUM ION, DNA (5'-D(*AP*GP*CP*AP*AP*(ORP)P*GP*GP*C)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2021-03-03
Release date:2021-11-17
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.667 Å)
Cite:Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites.
Nat Commun, 12, 2021
5UUG
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BU of 5uug by Molmil
Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (9-mer product complex)
Descriptor: CALCIUM ION, DNA (5'-D(*AP*GP*GP*CP*AP*(ORP)P*AP*GP*C)-3'), DNA (5'-D(*TP*GP*CP*TP*TP*TP*GP*CP*C)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2017-02-16
Release date:2017-07-19
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.712 Å)
Cite:Toxicity and repair of DNA adducts produced by the natural product yatakemycin.
Nat. Chem. Biol., 13, 2017
5CLC
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BU of 5clc by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer B)
Descriptor: AlkD, DNA (5'-D(*AP*AP*GP*CP*CP*(DZM)P*CP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*GP*TP*GP*GP*CP*T)-3')
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.729 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5KUB
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BU of 5kub by Molmil
Bacillus cereus DNA glycosylase AlkD bound to 7-methylguanine nucleobase and DNA containing an oxocarbenium-intermediate analog
Descriptor: 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one, DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*CP*TP*CP*TP*CP*GP*GP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2016-07-13
Release date:2016-09-14
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:A Catalytic Role for C-H/ pi Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD.
J.Am.Chem.Soc., 138, 2016
5CLE
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BU of 5cle by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic-site analog and a free 3-methyladenine nucleobase
Descriptor: 3-METHYL-3H-PURIN-6-YLAMINE, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(3DR)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
3JXZ
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BU of 3jxz by Molmil
Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from T)
Descriptor: DNA (5'-D(*AP*AP*AP*GP*CP*CP*TP*CP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3'), alkylpurine DNA glycosylase AlkD
Authors:Rubinson, E.H, Eichman, B.F.
Deposit date:2009-09-21
Release date:2010-09-22
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:An unprecedented nucleic acid capture mechanism for excision of DNA damage.
Nature, 468, 2010
3JY1
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BU of 3jy1 by Molmil
Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from C)
Descriptor: DNA (5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3'), alkylpurine DNA glycosylase AlkD
Authors:Rubinson, E.H, Eichman, B.F.
Deposit date:2009-09-21
Release date:2010-09-22
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.754 Å)
Cite:An unprecedented nucleic acid capture mechanism for excision of DNA damage.
Nature, 468, 2010
5CLB
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BU of 5clb by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer A)
Descriptor: AlkD, DNA (5'-D(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-3')
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.766 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
5CL4
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BU of 5cl4 by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (71% substrate/29% product at 24 hours)
Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.866 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
7LXJ
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BU of 7lxj by Molmil
Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-adenine nucleobase adduct and DNA containing an abasic site
Descriptor: CALCIUM ION, DNA (5'-D(*AP*GP*CP*AP*AP*(ORP)P*GP*GP*C)-3'), DNA (5'-D(*TP*GP*CP*CP*TP*TP*TP*GP*C)-3'), ...
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2021-03-03
Release date:2021-11-17
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites.
Nat Commun, 12, 2021
5CL3
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BU of 5cl3 by Molmil
Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (100% substrate at 4 hours)
Descriptor: AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')
Authors:Mullins, E.A, Eichman, B.F.
Deposit date:2015-07-16
Release date:2015-10-28
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.971 Å)
Cite:The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Nature, 527, 2015
3BVS
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BU of 3bvs by Molmil
Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD
Descriptor: Alkylpurine DNA Glycosylase AlkD
Authors:Rubinson, E.H, Eichman, B.F.
Deposit date:2008-01-07
Release date:2008-07-15
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:A New Protein Architecture for Processing Alkylation Damaged DNA: The Crystal Structure of DNA Glycosylase AlkD.
J.Mol.Biol., 381, 2008

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PDB entries from 2024-07-10

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