4QC7
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![BU of 4qc7 by Molmil](/molmil-images/mine/4qc7) | Dodecamer structure of 5-formylcytosine containing DNA | Descriptor: | short DNA strands | Authors: | Szulik, M.W, Pallan, P, Egli, M, Stone, M.P. | Deposit date: | 2014-05-09 | Release date: | 2015-02-11 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry, 54, 2015
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4NFL
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![BU of 4nfl by Molmil](/molmil-images/mine/4nfl) | Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor NPB-T | Descriptor: | 1-{2-deoxy-3,5-O-[(4-nitrophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 5'(3')-deoxyribonucleotidase, ... | Authors: | Pachl, P, Rezacova, P, Brynda, J. | Deposit date: | 2013-10-31 | Release date: | 2014-09-10 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.375 Å) | Cite: | Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases. Org.Biomol.Chem., 12, 2014
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1MWJ
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![BU of 1mwj by Molmil](/molmil-images/mine/1mwj) | Crystal Structure of a MUG-DNA pseudo substrate complex | Descriptor: | 5'-D(*CP*GP*CP*GP*A*GP*(DU)P*TP*CP*GP*CP*G)-3', G/U mismatch-specific DNA glycosylase | Authors: | Barrett, T.E, Scharer, O, Savva, R, Brown, T, Jiricny, J, Verdine, G.L, Pearl, L.H. | Deposit date: | 2002-09-30 | Release date: | 2002-10-11 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Crystal Structure of a thwarted mismatch glycosylase DNA repair complex Embo J., 18, 1999
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7YGP
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![BU of 7ygp by Molmil](/molmil-images/mine/7ygp) | DNA duplex containing 5OHU-T base pairs | Descriptor: | COBALT (II) ION, COBALT HEXAMMINE(III), DNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3') | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | Deposit date: | 2022-07-12 | Release date: | 2023-05-24 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.997 Å) | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem., 241, 2023
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7YGO
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![BU of 7ygo by Molmil](/molmil-images/mine/7ygo) | DNA duplex containing 5OHU-Hg(II)-T base pairs | Descriptor: | DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3'), MERCURY (II) ION | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | Deposit date: | 2022-07-12 | Release date: | 2023-05-24 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.403 Å) | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem., 241, 2023
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3JAA
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![BU of 3jaa by Molmil](/molmil-images/mine/3jaa) | HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM) | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, DNA (5'-D(*T*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3, DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3'), ... | Authors: | Lau, W.C.Y, Li, Y, Zhang, Q, Huen, M.S.Y. | Deposit date: | 2015-05-19 | Release date: | 2015-12-23 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (22 Å) | Cite: | Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA Sci Rep, 5, 2015
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3N4O
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![BU of 3n4o by Molmil](/molmil-images/mine/3n4o) | Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one | Descriptor: | 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, 5'-D(*CP*GP*CP*GP*AP*AP*TP*(B7C)P*CP*GP*CP*G)-3' | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S. | Deposit date: | 2010-05-22 | Release date: | 2010-08-11 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one. Nucleic Acids Res., 2010
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3N4N
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![BU of 3n4n by Molmil](/molmil-images/mine/3n4n) | Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*A)-3', 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3' | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S. | Deposit date: | 2010-05-22 | Release date: | 2010-08-11 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.92 Å) | Cite: | Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one. Nucleic Acids Res., 2010
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1VJ4
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![BU of 1vj4 by Molmil](/molmil-images/mine/1vj4) | SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C) | Descriptor: | 5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3' | Authors: | Shakked, Z, Rabinovich, D, Kennard, O, Cruse, W.B, Salisbury, S.A, Viswamitra, M.A. | Deposit date: | 1989-01-11 | Release date: | 1989-01-11 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C) J.Mol.Biol., 166, 1983
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3OPI
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![BU of 3opi by Molmil](/molmil-images/mine/3opi) | 7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION, SODIUM ION | Authors: | Kowal, E.A, Ganguly, M, Pallan, P.S, Marky, L.A, Gold, B, Egli, M, Stone, M.P. | Deposit date: | 2010-09-01 | Release date: | 2011-08-31 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-deoxyadenosine:dT Base Pairing in DNA. J.Phys.Chem.B, 115, 2011
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3PF4
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![BU of 3pf4 by Molmil](/molmil-images/mine/3pf4) | Crystal structure of Bs-CspB in complex with r(GUCUUUA) | Descriptor: | Cold shock protein cspB, MAGNESIUM ION, SODIUM ION, ... | Authors: | Sachs, R, Max, K.E.A, Heinemann, U. | Deposit date: | 2010-10-27 | Release date: | 2011-09-21 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.38 Å) | Cite: | RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution. Rna, 18, 2012
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3PF5
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![BU of 3pf5 by Molmil](/molmil-images/mine/3pf5) | |
4I9V
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![BU of 4i9v by Molmil](/molmil-images/mine/4i9v) | The atomic structure of 5-Hydroxymethyl 2'-deoxycitidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5HC)P*GP*CP*G)-3'), MAGNESIUM ION, SPERMINE (FULLY PROTONATED FORM) | Authors: | Nocek, B, Szulik, M.W, Joachimiak, A, Stone, M.P. | Deposit date: | 2012-12-05 | Release date: | 2013-11-20 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.02 Å) | Cite: | Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry, 54, 2015
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3RDP
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![BU of 3rdp by Molmil](/molmil-images/mine/3rdp) | Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-METHYL-FHBT | Descriptor: | 6-[(2R)-2-(fluoromethyl)-3-hydroxy-propyl]-1,5-dimethyl-pyrimidine-2,4-dione, SULFATE ION, Thymidine kinase | Authors: | Pernot, L, Perozzo, R, Westermaier, Y, Martic, M, Ametamey, S, Scapozza, L. | Deposit date: | 2011-04-01 | Release date: | 2011-08-03 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo. Nucleosides Nucleotides Nucleic Acids, 30, 2011
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4L6C
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![BU of 4l6c by Molmil](/molmil-images/mine/4l6c) | Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pib-t | Descriptor: | 1,2-ETHANEDIOL, 1-{2-deoxy-3,5-O-[(4-iodophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione, 5'(3')-deoxyribonucleotidase, ... | Authors: | Pachl, P, Brynda, J, Rezacova, P. | Deposit date: | 2013-06-12 | Release date: | 2014-09-10 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases. Org.Biomol.Chem., 12, 2014
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2Z70
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![BU of 2z70 by Molmil](/molmil-images/mine/2z70) | E.coli RNase 1 in complex with d(CGCGATCGCG) | Descriptor: | CALCIUM ION, DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DTP*DCP*DGP*DCP*DG)-3'), Ribonuclease I | Authors: | Martinez-Rodriguez, S, Loris, R, Messens, J. | Deposit date: | 2007-08-09 | Release date: | 2008-06-24 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli Protein Sci., 17, 2008
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1DA0
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![BU of 1da0 by Molmil](/molmil-images/mine/1da0) | DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN | Descriptor: | DAUNOMYCIN, DNA (5'-D(*CP*GP*AP*TP*CP*G)-3') | Authors: | Moore, M.H, Hunter, W.N, Langlois D'Estaintot, B, Kennard, O. | Deposit date: | 1992-10-17 | Release date: | 1993-07-15 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | DNA-drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin. J.Mol.Biol., 206, 1989
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2UVR
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![BU of 2uvr by Molmil](/molmil-images/mine/2uvr) | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | Authors: | Irimia, A, Egli, M. | Deposit date: | 2007-03-13 | Release date: | 2007-05-08 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4. J.Biol.Chem., 282, 2007
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1D90
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![BU of 1d90 by Molmil](/molmil-images/mine/1d90) | REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH I.T MISMATCHED BASE PAIRS | Descriptor: | DNA (5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3') | Authors: | Cruse, W.B.T, Aymani, J, Kennard, O, Brown, T, Jack, A.G.C, Leonard, G.A. | Deposit date: | 1992-10-17 | Release date: | 1993-07-15 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs. Nucleic Acids Res., 17, 1989
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2UVW
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![BU of 2uvw by Molmil](/molmil-images/mine/2uvw) | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | Authors: | Irimia, A, Egli, M. | Deposit date: | 2007-03-14 | Release date: | 2007-05-08 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4. J.Biol.Chem., 282, 2007
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2UVU
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![BU of 2uvu by Molmil](/molmil-images/mine/2uvu) | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | Authors: | Irimia, A, Egli, M. | Deposit date: | 2007-03-14 | Release date: | 2007-05-08 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4. J.Biol.Chem., 282, 2007
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2UVV
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![BU of 2uvv by Molmil](/molmil-images/mine/2uvv) | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | Authors: | Irimia, A, Egli, M. | Deposit date: | 2007-03-14 | Release date: | 2007-05-08 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4. J.Biol.Chem., 282, 2007
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4H10
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![BU of 4h10 by Molmil](/molmil-images/mine/4h10) | |
4HQI
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![BU of 4hqi by Molmil](/molmil-images/mine/4hqi) | Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex | Descriptor: | SPERMINE, STRONTIUM ION, Short modified nucleic acids | Authors: | Kowal, E.A, Lad, R, Pallan, P.S, Muffly, E, Wawrzak, Z, Egli, M, Sturla, S.J, Stone, M.P. | Deposit date: | 2012-10-25 | Release date: | 2013-07-10 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Nucleic Acids Res., 41, 2013
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1MRN
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![BU of 1mrn by Molmil](/molmil-images/mine/1mrn) | CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH BISUBSTRATE INHIBITOR (TP5A) | Descriptor: | MAGNESIUM ION, P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE, SULFATE ION, ... | Authors: | Haouz, A, Vanheusden, V, Munier-Lehmann, H, Froeyen, M, Herdewijn, P, Van Calenbergh, S, Delarue, M. | Deposit date: | 2002-09-18 | Release date: | 2003-01-07 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism. J.Biol.Chem., 278, 2003
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