Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

6BOR
DownloadVisualize
BU of 6bor by Molmil
Human APE1 substrate complex with an G/G mismatch adjacent the THF
Descriptor: 1,2-ETHANEDIOL, 21-mer DNA, CHLORIDE ION, ...
Authors:Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S.
Deposit date:2017-11-20
Release date:2018-08-15
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Acta Crystallogr D Struct Biol, 74, 2018
5CFG
DownloadVisualize
BU of 5cfg by Molmil
C2 crystal form of APE1 with Mg2+
Descriptor: DNA-(apurinic or apyrimidinic site) lyase, MAGNESIUM ION
Authors:Morera, S, Vigouroux, A.
Deposit date:2015-07-08
Release date:2016-07-06
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.
Biochimie, 128-129, 2016
4C1R
DownloadVisualize
BU of 4c1r by Molmil
Bacteroides thetaiotaomicron VPI-5482 mannosyl-6-phosphatase Bt3783
Descriptor: 1,2-ETHANEDIOL, MAGNESIUM ION, MANNOSYL-6-PHOSPHATASE
Authors:Cuskin, F, Lowe, E.C, Zhu, Y, Temple, M, Thompson, A.J, Cartmell, A, Piens, K, Bracke, D, Vervecken, W, Munoz-Munoz, J.L, Suits, M.D.L, Boraston, A.B, Williams, S.J, Davies, G.J, Abbott, W.D, Martens, E.C, Gilbert, H.J.
Deposit date:2013-08-13
Release date:2013-11-13
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism.
Nature, 517, 2015
5DFH
DownloadVisualize
BU of 5dfh by Molmil
Human APE1 mismatch product complex
Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
Authors:Freudenthal, B.D, Wilson, S.H.
Deposit date:2015-08-26
Release date:2015-10-14
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.949 Å)
Cite:Capturing snapshots of APE1 processing DNA damage.
Nat.Struct.Mol.Biol., 22, 2015
5DFJ
DownloadVisualize
BU of 5dfj by Molmil
Human APE1 E96Q/D210N mismatch substrate complex
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Freudenthal, B.D, Wilson, S.H.
Deposit date:2015-08-26
Release date:2015-10-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Capturing snapshots of APE1 processing DNA damage.
Nat.Struct.Mol.Biol., 22, 2015
4FVA
DownloadVisualize
BU of 4fva by Molmil
Crystal structure of truncated Caenorhabditis elegans TDP2
Descriptor: 1,2-ETHANEDIOL, 5'-tyrosyl-DNA phosphodiesterase, MAGNESIUM ION, ...
Authors:Shi, K, Kurahashi, K, Aihara, H.
Deposit date:2012-06-29
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
6CA4
DownloadVisualize
BU of 6ca4 by Molmil
Crystal structure of humanized D. rerio TDP2 by 14 mutations
Descriptor: 1,2-ETHANEDIOL, MAGNESIUM ION, MALONATE ION, ...
Authors:Shi, K, Aihrara, H.
Deposit date:2018-01-29
Release date:2018-05-02
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.623 Å)
Cite:New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2).
Eur J Pharm Sci, 118, 2018
6BOV
DownloadVisualize
BU of 6bov by Molmil
Human APE1 substrate complex with an A/G mismatch adjacent the THF
Descriptor: 21-mer DNA, DI(HYDROXYETHYL)ETHER, DNA-(apurinic or apyrimidinic site) lyase
Authors:Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S.
Deposit date:2017-11-20
Release date:2018-08-15
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.975 Å)
Cite:Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Acta Crystallogr D Struct Biol, 74, 2018
5DG0
DownloadVisualize
BU of 5dg0 by Molmil
Human APE1 phosphorothioate substrate complex with Mn2+
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(OMC)P*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Freudenthal, B.D, Wilson, S.H.
Deposit date:2015-08-27
Release date:2015-10-14
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Capturing snapshots of APE1 processing DNA damage.
Nat.Struct.Mol.Biol., 22, 2015
5DFI
DownloadVisualize
BU of 5dfi by Molmil
Human APE1 phosphorothioate substrate complex
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(OMC)P*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Freudenthal, B.D, Wilson, S.H.
Deposit date:2015-08-26
Release date:2015-10-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.63 Å)
Cite:Capturing snapshots of APE1 processing DNA damage.
Nat.Struct.Mol.Biol., 22, 2015
4AWN
DownloadVisualize
BU of 4awn by Molmil
Structure of recombinant human DNase I (rhDNaseI) in complex with Magnesium and Phosphate.
Descriptor: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Parsiegla, G, Noguere, C, Santell, L, Lazarus, R.A, Bourne, Y.
Deposit date:2012-06-04
Release date:2013-01-09
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:The Structure of Human DNase I Bound to Magnesium and Phosphate Ions Points to a Catalytic Mechanism Common to Members of the DNase I-Like Superfamily.
Biochemistry, 51, 2012
4B5H
DownloadVisualize
BU of 4b5h by Molmil
Substate bound inactive mutant of Neisseria AP endonuclease in presence of metal ions
Descriptor: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP*3DRP*CP*AP*TP*CP*GP)-3', MANGANESE (II) ION, ...
Authors:Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S.
Deposit date:2012-08-03
Release date:2012-10-17
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (3.05 Å)
Cite:Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Proc. Natl. Acad. Sci. U.S.A., 109, 2012
4B5M
DownloadVisualize
BU of 4b5m by Molmil
Neisseria AP endonuclease bound to the substrate with a cytosine orphan base
Descriptor: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3', 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP)-3', ...
Authors:Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S.
Deposit date:2012-08-06
Release date:2012-10-17
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (2.758 Å)
Cite:Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Proc. Natl. Acad. Sci. U.S.A., 109, 2012
4GZ0
DownloadVisualize
BU of 4gz0 by Molmil
Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex
Descriptor: 1,2-ETHANEDIOL, 6-aminohexan-1-ol, ACETATE ION, ...
Authors:Schellenberg, M.J, Williams, R.S.
Deposit date:2012-09-05
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.113 Å)
Cite:Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012
4CMN
DownloadVisualize
BU of 4cmn by Molmil
Crystal structure of OCRL in complex with a phosphate ion
Descriptor: GLYCEROL, INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1, MAGNESIUM ION, ...
Authors:Tresaugues, L, Moche, M, Arrowsmith, C.H, Berglund, H, Bountra, C, Edwards, A.M, Ekblad, T, Flodin, S, Graslund, S, Karlberg, T, Nyman, T, Schuler, H, Silvander, C, Thorsell, A.G, Weigelt, J, Welin, M, Nordlund, P.
Deposit date:2014-01-16
Release date:2014-04-16
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (3.13 Å)
Cite:Structural Basis for Phosphoinositide Substrate Recognition, Catalysis, and Membrane Interactions in Human Inositol Polyphosphate 5-Phosphatases.
Structure, 22, 2014
6BOW
DownloadVisualize
BU of 6bow by Molmil
Human APE1 substrate complex with an T/T mismatch adjacent the THF
Descriptor: 21-mer DNA, DNA-(apurinic or apyrimidinic site) lyase
Authors:Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S.
Deposit date:2017-11-20
Release date:2018-08-15
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.59 Å)
Cite:Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Acta Crystallogr D Struct Biol, 74, 2018
4GZ1
DownloadVisualize
BU of 4gz1 by Molmil
Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3'), FORMIC ACID, ...
Authors:Schellenberg, M.J, Williams, R.S.
Deposit date:2012-09-05
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012
4GYZ
DownloadVisualize
BU of 4gyz by Molmil
Mus Musculus Tdp2 Bound to dAMP and Mg2+
Descriptor: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE, CHLORIDE ION, MAGNESIUM ION, ...
Authors:Schellenberg, M.J, Williams, R.S.
Deposit date:2012-09-05
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.556 Å)
Cite:Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012
5DV2
DownloadVisualize
BU of 5dv2 by Molmil
Crystal structure of human CNOT6L in complex with cytidine-5'-monophosphate
Descriptor: CCR4-NOT transcription complex subunit 6-like, CYTIDINE-5'-MONOPHOSPHATE
Authors:Zhang, Q, Bartlam, M.
Deposit date:2015-09-21
Release date:2016-05-18
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Structural basis for inhibition of the deadenylase activity of human CNOT6L
Febs Lett., 590, 2016
6BOQ
DownloadVisualize
BU of 6boq by Molmil
Human APE1 substrate complex with an A/A mismatch adjacent the THF
Descriptor: 1,2-ETHANEDIOL, 21-mer DNA, DNA-(apurinic or apyrimidinic site) lyase
Authors:Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S.
Deposit date:2017-11-20
Release date:2018-08-15
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.96 Å)
Cite:Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Acta Crystallogr D Struct Biol, 74, 2018
5DFF
DownloadVisualize
BU of 5dff by Molmil
Human APE1 product complex
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ...
Authors:Freudenthal, B.D, Wilson, S.H.
Deposit date:2015-08-26
Release date:2015-10-14
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (1.57 Å)
Cite:Capturing snapshots of APE1 processing DNA damage.
Nat.Struct.Mol.Biol., 22, 2015
4FPV
DownloadVisualize
BU of 4fpv by Molmil
Crystal structure of D. rerio TDP2 complexed with single strand DNA product
Descriptor: DNA (5'-D(P*TP*GP*CP*AP*G)-3'), GLYCEROL, MAGNESIUM ION, ...
Authors:Shi, K, Kurahashi, K, Aihara, H.
Deposit date:2012-06-22
Release date:2012-10-31
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
5DV4
DownloadVisualize
BU of 5dv4 by Molmil
Crystal structure of human CNOT6L in complex with neomycin
Descriptor: CCR4-NOT transcription complex subunit 6-like, NEOMYCIN, SULFATE ION
Authors:Zhang, Q, Bartlam, M.
Deposit date:2015-09-21
Release date:2016-10-26
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural basis for inhibition of the deadenylase activity of human CNOT6L
Febs Lett., 590, 2016
6BT1
DownloadVisualize
BU of 6bt1 by Molmil
Structure of the human Nocturnin catalytic domain
Descriptor: MAGNESIUM ION, Nocturnin
Authors:Abshire, E.T, Chasseur, J, Del Rizzo, P, Trievel, R.
Deposit date:2017-12-04
Release date:2018-05-16
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.48 Å)
Cite:The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells.
Nucleic Acids Res., 46, 2018
4GZ2
DownloadVisualize
BU of 4gz2 by Molmil
Mus Musculus Tdp2 excluded ssDNA complex
Descriptor: DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3'), FORMIC ACID, MAGNESIUM ION, ...
Authors:Schellenberg, M.J, Williams, R.S.
Deposit date:2012-09-05
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012

226707

PDB entries from 2024-10-30

PDB statisticsPDBj update infoContact PDBjnumon