Author results

4F1H
  • Download 4f1h
  • View 4f1h
Molmil generated image of 4f1h
CRYSTAL STRUCTURE OF TDP2 FROM DANIO RERIO COMPLEXED WITH A SINGLE STRAND DNA
Descriptor:DNA (5'-D(P*TP*GP*CP*AP*G)-3'), Tyrosyl-DNA phosphodiesterase 2, PHOSPHATE ION, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2012-05-06
Release date:2012-10-31
Last modified:2013-01-02
Method:X-RAY DIFFRACTION (1.662 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
4F1I
  • Download 4f1i
  • View 4f1i
Molmil generated image of 4f1i
CRYSTAL STRUCTURE OF SEMET TDP2 FROM CAENORHABDITIS ELEGANS
Descriptor:5'-tyrosyl-DNA phosphodiesterase, GLYCEROL
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2012-05-07
Release date:2012-10-31
Last modified:2017-11-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
4FPV
  • Download 4fpv
  • View 4fpv
Molmil generated image of 4fpv
CRYSTAL STRUCTURE OF D. RERIO TDP2 COMPLEXED WITH SINGLE STRAND DNA PRODUCT
Descriptor:Tyrosyl-DNA phosphodiesterase 2, DNA (5'-D(P*TP*GP*CP*AP*G)-3'), SODIUM ION, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2012-06-22
Release date:2012-10-31
Last modified:2017-11-15
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
4FVA
  • Download 4fva
  • View 4fva
Molmil generated image of 4fva
CRYSTAL STRUCTURE OF TRUNCATED CAENORHABDITIS ELEGANS TDP2
Descriptor:5'-tyrosyl-DNA phosphodiesterase, 1,2-ETHANEDIOL, MAGNESIUM ION, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2012-06-29
Release date:2012-10-31
Last modified:2013-01-02
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
4GEW
  • Download 4gew
  • View 4gew
Molmil generated image of 4gew
CRYSTAL STRUCTURE OF TDP2 FROM C. ELEGANS
Descriptor:5'-tyrosyl-DNA phosphodiesterase, GLYCEROL
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2012-08-02
Release date:2012-10-31
Last modified:2013-01-02
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
5CQD
  • Download 5cqd
  • View 5cqd
Molmil generated image of 5cqd
CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC->dU-editing enzyme APOBEC-3B, ZINC ION, GLYCEROL
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2015-07-21
Release date:2015-10-07
Last modified:2017-09-27
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
J.Biol.Chem., 290, 2015
5CQH
  • Download 5cqh
  • View 5cqh
Molmil generated image of 5cqh
CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC-dU-editing enzyme APOBEC-3B, ZINC ION, 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2015-07-21
Release date:2015-10-07
Last modified:2017-09-27
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
J.Biol.Chem., 290, 2015
5CQI
  • Download 5cqi
  • View 5cqi
Molmil generated image of 5cqi
CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC-dU-editing enzyme APOBEC-3B, ZINC ION, GLYCEROL
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2015-07-21
Release date:2015-10-07
Last modified:2015-12-02
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
J.Biol.Chem., 290, 2015
5CQK
  • Download 5cqk
  • View 5cqk
Molmil generated image of 5cqk
CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC->dU-editing enzyme APOBEC-3B, ZINC ION, GLYCEROL, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2015-07-21
Release date:2015-10-07
Last modified:2015-12-02
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
J.Biol.Chem., 290, 2015
5SWW
  • Download 5sww
  • View 5sww
Molmil generated image of 5sww
CRYSTAL STRUCTURE OF HUMAN APOBEC3A COMPLEXED WITH SSDNA
Descriptor:DNA dC->dU-editing enzyme APOBEC-3A, DNA 15-Mer, ZINC ION, ...
Authors:Shi, K., Banerjee, S., Kurahashi, K., Aihara, H.
Deposit date:2016-08-09
Release date:2016-12-28
Last modified:2017-09-20
Method:X-RAY DIFFRACTION (3.151 Å)
Cite:Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Nat. Struct. Mol. Biol., 24, 2017
5SXG
  • Download 5sxg
  • View 5sxg
Molmil generated image of 5sxg
CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC->dU-editing enzyme APOBEC-3B, ZINC ION, 1,3-PROPANDIOL, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2016-08-09
Release date:2017-12-27
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Sci Rep, 7, 2017
5SXH
  • Download 5sxh
  • View 5sxh
Molmil generated image of 5sxh
CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC->dU-editing enzyme APOBEC-3B, ZINC ION, ethane-1,2-diol
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2016-08-09
Release date:2017-12-27
Last modified:2018-04-18
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Sci Rep, 7, 2017
5TD5
  • Download 5td5
  • View 5td5
Molmil generated image of 5td5
CRYSTAL STRUCTURE OF HUMAN APOBEC3B VARIANT COMPLEXED WITH SSDNA
Descriptor:DNA dC->dU-editing enzyme APOBEC-3B, DNA (5'-D(P*TP*TP*CP*AP*T)-3'), ZINC ION, ...
Authors:Shi, K., Banerjee, S., Kurahashi, K., Aihara, H.
Deposit date:2016-09-16
Release date:2016-12-28
Last modified:2017-02-22
Method:X-RAY DIFFRACTION (1.718 Å)
Cite:Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Nat. Struct. Mol. Biol., 24, 2017
5WFY
  • Download 5wfy
  • View 5wfy
Molmil generated image of 5wfy
CRYSTAL STRUCTURE OF DNA-BINDING DOMAIN OF THE BACTERIOPHAGE T4 LIGASE
Descriptor:DNA ligase, GLYCEROL
Authors:Shi, K., Aihara, H.
Deposit date:2017-07-13
Release date:2018-09-26
Last modified:2018-11-14
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46, 2018
6DRT
  • Download 6drt
  • View 6drt
Molmil generated image of 6drt
CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP GP45 COMPLEXED WITH RECOGNITION PEPTIDE OF LIGASE FROM BACTERIOPHAGE T4
Descriptor:DNA polymerase clamp, GP45 recognition loop, 1,2-ETHANEDIOL
Authors:Shi, K., Aihara, H.
Deposit date:2018-06-13
Release date:2018-09-26
Last modified:2018-11-14
Method:X-RAY DIFFRACTION (2.117 Å)
Cite:T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46, 2018
6DT1
  • Download 6dt1
  • View 6dt1
Molmil generated image of 6dt1
CRYSTAL STRUCTURE OF THE LIGASE FROM BACTERIOPHAGE T4 COMPLEXED WITH DNA INTERMEDIATE
Descriptor:DNA ligase, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3'), DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3'), ...
Authors:Shi, K., Aihara, H.
Deposit date:2018-06-14
Release date:2018-09-19
Last modified:2018-11-14
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46, 2018
1DVL
  • Download 1dvl
  • View 1dvl
Molmil generated image of 1dvl
CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END
Descriptor:5'-D(*CP*CP*IP*IP*CP*IP*CP*CP*IP*I)-3', NETROPSIN
Authors:Shi, K., Mitra, S.N., Sundaralingam, M.
Deposit date:2000-01-21
Release date:2002-03-29
Last modified:2017-10-04
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin.
Acta Crystallogr.,Sect.D, 58, 2002
1JO2
  • Download 1jo2
  • View 1jo2
Molmil generated image of 1jo2
CRYSTAL STRUCTURE OF THE B-DNA HEXAMER (CGATCG).DAUNOMYCIN COMPLEX CONTAINING A RIBOSE AT THE INTERCALATION SITE
Descriptor:5'-D(*C)-R(P*G)-D(P*AP*TP*CP*G)-3', DAUNOMYCIN
Authors:Shi, K., Pan, B., Sundaralingam, M.
Deposit date:2001-07-26
Release date:2003-07-29
Last modified:2017-10-04
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution.
Acta Crystallogr.,Sect.D, 59, 2003
1L3Z
  • Download 1l3z
  • View 1l3z
Molmil generated image of 1l3z
CRYSTAL STRUCTURE ANALYSIS OF AN RNA HEPTAMER
Descriptor:5'-R(*GP*UP*AP*UP*AP*CP*A)-3', SODIUM ION
Authors:Shi, K., Pan, B., Sundaralingam, M.
Deposit date:2002-03-04
Release date:2003-02-25
Last modified:2018-03-07
Method:X-RAY DIFFRACTION (2.01 Å)
Cite:The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs
Nucleic Acids Res., 31, 2003
1R3Z
  • Download 1r3z
  • View 1r3z
Molmil generated image of 1r3z
CRYSTAL STRUCTURES OF D(GM5CGM5CGCGC) AND D(GCGCGM5CGM5C): EFFECTS OF METHYLATION ON ALTERNATING DNA OCTAMERS
Descriptor:5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*C)-3'
Authors:Shi, K., Pan, B., Tippin, D., Sundaralingam, M.
Deposit date:2003-10-03
Release date:2003-12-23
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
Acta Crystallogr.,Sect.D, 60, 2004
1R41
  • Download 1r41
  • View 1r41
Molmil generated image of 1r41
CRYSTAL STRUCTURES OF D(GM5CGM5CGCGC) AND D(GCGCGM5CGM5C): EFFECTS OF METHYLATION ON ALTERNATING DNA OCTAMERS
Descriptor:5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3'
Authors:Shi, K., Pan, B., Tippin, D., Sundaralingam, M.
Deposit date:2003-10-03
Release date:2003-12-23
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
Acta Crystallogr.,Sect.D, 60, 2004
2AW6
  • Download 2aw6
  • View 2aw6
Molmil generated image of 2aw6
STRUCTURE OF A BACTERIAL PEPTIDE PHEROMONE/RECEPTOR COMPLEX AND ITS MECHANISM OF GENE REGULATION
Descriptor:PrgX, peptide
Authors:Shi, K., Brown, C.K., Gu, Z.Y., Kozlowicz, B.K., Dunny, G.M., Ohlendorf, D.H., Earhart, C.A.
Deposit date:2005-08-31
Release date:2005-12-06
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis.
Proc.Natl.Acad.Sci.Usa, 102, 2005
2AWI
  • Download 2awi
  • View 2awi
Molmil generated image of 2awi
STRUCTURE OF PRGX Y153C MUTANT
Descriptor:PrgX
Authors:Shi, K., Brown, C.K., Gu, Z.Y., Kozlowicz, B.k., Dunny, G.M., Ohlendorf, D.H., Earhart, C.A.
Deposit date:2005-09-01
Release date:2005-12-06
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis.
Proc.Natl.Acad.Sci.Usa, 102, 2005
2AXU
  • Download 2axu
  • View 2axu
Molmil generated image of 2axu
STRUCTURE OF PRGX
Descriptor:PrgX
Authors:Shi, K., Brown, C.K., Gu, Z.Y., Kozlowicz, B.K., Dunny, G.M., Ohlendorf, D.H., Earhart, C.A.
Deposit date:2005-09-06
Release date:2005-12-06
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis.
Proc.Natl.Acad.Sci.Usa, 102, 2005
2AXV
  • Download 2axv
  • View 2axv
Molmil generated image of 2axv
STRUCTURE OF PRGX Y153C MUTANT
Descriptor:PrgX
Authors:Shi, K., Brown, C.K., Gu, Z.Y., Kozlowicz, B.K., Dunny, G.M., Ohlendorf, D.H., Earhart, C.A.
Deposit date:2005-09-06
Release date:2005-12-06
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis.
Proc.Natl.Acad.Sci.Usa, 102, 2005