3MWS
 
 | | Crystal Structure of Group N HIV-1 Protease | | Descriptor: | (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE, CHLORIDE ION, HIV-1 Protease | | Authors: | Sayer, J.M, Agniswamy, J, Weber, I.T, Louis, J.M. | | Deposit date: | 2010-05-06 | | Release date: | 2011-03-23 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.09 Å) | | Cite: | Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: relevance to drug resistance.
Protein Sci., 19, 2010
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1BPS
 | | MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3'), DNA (5'-D(*GP*GP*TP*CP*(BAP)AP*CP*GP*AP*G)-3') | | Authors: | Schwartz, J.S, Rice, J.S, Luxon, B.A, Sayer, J.M, Xie, G, Yeh, H.J.C, Liu, X, Jerina, D.M, Gorenstein, D.G. | | Deposit date: | 1998-08-06 | | Release date: | 1998-08-19 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine.
Biochemistry, 36, 1997
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3UCB
 | | Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 in Complex with Darunavir | | Descriptor: | (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE, Protease | | Authors: | Agniswamy, J, Chen-Hsiang, S, Aniana, A, Sayer, J.M, Louis, J.M, Weber, I.T. | | Deposit date: | 2011-10-26 | | Release date: | 2012-03-28 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements.
Biochemistry, 51, 2012
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3UFN
 | | Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 in Complex with Saquinavir | | Descriptor: | (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide, CHLORIDE ION, HIV-1 protease | | Authors: | Agniswamy, J, Chen-Hsiang, S, Aniana, A, Sayer, J.M, Louis, J.M, Weber, I.T. | | Deposit date: | 2011-11-01 | | Release date: | 2012-03-28 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements.
Biochemistry, 51, 2012
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3UF3
 | | Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical isolate PR20 | | Descriptor: | GLYCEROL, HIV-1 protease, YTTRIUM ION | | Authors: | Agniswamy, J, Chen-Hsiang, S, Aniana, A, Sayer, J.M, Louis, J.M, Weber, I.T. | | Deposit date: | 2011-10-31 | | Release date: | 2012-03-28 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.63 Å) | | Cite: | HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements.
Biochemistry, 51, 2012
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1JDG
 | | Solution Structure of a Trans-Opened (10S)-dA Adduct of (+)-(7S,8R,9S,10R)-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully Complementary DNA Duplex | | Descriptor: | 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3', 5'-D(*CP*GP*GP*TP*CP*(BPA)AP*CP*GP*AP*GP*G)-3', 7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE | | Authors: | Pradhan, P, Tirumala, S, Liu, X, Sayer, J.M, Jerina, D.M, Yeh, H.J.C. | | Deposit date: | 2001-06-13 | | Release date: | 2001-07-04 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Solution structure of a trans-opened (10S)-dA adduct of (+)-(7S,8R,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully complementary DNA duplex: evidence for a major syn conformation.
Biochemistry, 40, 2001
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2ROU
 | | Stereospecific Conformations of N2-dG 1R-trans-anti-Benzo[c]phenanthrene DNA Adducts: 3'-Intercalation of the 1R Adduct and 5'-Minor Groove Orientation of the 1S Adduct in an Iterated (CG)3 Repeat | | Descriptor: | (1R)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-TRIOL, DNA (5'-D(*DAP*DTP*DCP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DAP*DTP*DG)-3'), DNA (5'-D(*DCP*DAP*DTP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DGP*DAP*DT)-3') | | Authors: | Wang, Y, Kroth, H, Yagi, H, Sayer, J.M, Kumar, S, Jerina, D.M, Stone, M.P. | | Deposit date: | 2008-04-20 | | Release date: | 2009-03-03 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | 3'-Intercalation of a N2-dG 1R-trans-anti-benzo[c]phenanthrene DNA adduct in an iterated (CG)3 repeat
Chem.Res.Toxicol., 21, 2008
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2LZK
 | | NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing | | Descriptor: | (11S,12S,13S)-11,12,13,14-tetrahydronaphtho[1,2,3,4-pqr]tetraphene-11,12,13-triol, DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'), DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3') | | Authors: | Tang, Y, Liu, Z, Ding, S, Lin, C.H, Cai, Y, Rodriguez, F.A, Sayer, J.M, Jerina, D.M, Amin, S, Broyde, S, Geacintov, N.E. | | Deposit date: | 2012-10-04 | | Release date: | 2012-11-21 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Nuclear Magnetic Resonance Solution Structure of an N(2)-Guanine DNA Adduct Derived from the Potent Tumorigen Dibenzo[a,l]pyrene: Intercalation from the Minor Groove with Ruptured Watson-Crick Base Pairing.
Biochemistry, 51, 2012
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3TKG
 | | crystal structure of HIV model protease precursor/saquinavir complex | | Descriptor: | (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide, CHLORIDE ION, GLYCEROL, ... | | Authors: | Agniswamy, J, Sayer, J, Weber, I, Louis, J. | | Deposit date: | 2011-08-26 | | Release date: | 2012-04-25 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.36 Å) | | Cite: | Terminal interface conformations modulate dimer stability prior to amino terminal autoprocessing of HIV-1 protease.
Biochemistry, 51, 2012
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3TKW
 | | Crystal structure of HIV protease model precursor/Darunavir complex | | Descriptor: | (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE, CHLORIDE ION, GLYCEROL, ... | | Authors: | Agniswamy, J, Sayer, J, Weber, I, Louis, J. | | Deposit date: | 2011-08-29 | | Release date: | 2012-04-25 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Terminal interface conformations modulate dimer stability prior to amino terminal autoprocessing of HIV-1 protease.
Biochemistry, 51, 2012
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1N8C
 | | Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex | | Descriptor: | (9S,10R)-9-HYDROXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE, 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3', 5'-D(*CP*GP*GP*TP*CP*AP*CP*GP*AP*GP*G)-3' | | Authors: | Volk, D.E, Thiviyanathan, V, Rice, J.S, Luxon, B.A, Shah, J.H, Yagi, H, Sayer, J.M, Yeh, H.J.C, Jerina, D.M, Gorenstein, D.G. | | Deposit date: | 2002-11-20 | | Release date: | 2003-02-14 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex
Biochemistry, 42, 2003
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1S0M
 | | Crystal structure of a Benzo[a]pyrene Diol Epoxide adduct in a ternary complex with a DNA polymerase | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*T)-3', ... | | Authors: | Ling, H, Sayer, J.M, Boudsocq, F, Plosky, B.S, Woodgate, R, Yang, W. | | Deposit date: | 2003-12-31 | | Release date: | 2004-03-30 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase.
Proc.Natl.Acad.Sci.USA, 101, 2004
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1N5Y
 | | HIV-1 Reverse Transcriptase Crosslinked to Post-Translocation AZTMP-Terminated DNA (Complex P) | | Descriptor: | 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3', 5'-D(*AP*TP*GP*C*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3', MAGNESIUM ION, ... | | Authors: | Sarafianos, S.G, Clark Jr, A.D, Das, K, Tuske, S, Birktoft, J.J, Ilankumaran, P, Ramesha, A.R, Sayer, J.M, Jerina, D.M, Boyer, P.L, Hughes, S.H, Arnold, E. | | Deposit date: | 2002-11-07 | | Release date: | 2003-01-28 | | Last modified: | 2021-10-27 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Structure of HIV-1 Reverse Transcriptase with Pre-Translocation and Post-Translocation AZTMP-Terminated DNA
Embo J., 21, 2002
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1N6Q
 | | HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA (complex N) | | Descriptor: | 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*AP*(ATM))-3', 5'-D(*AP*T*GP*CP*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3', MAGNESIUM ION, ... | | Authors: | Sarafianos, S.G, Clark Jr, A.D, Das, K, Tuske, S, Birktoft, J.J, Ilankumaran, I, Ramesha, A.R, Sayer, J.M, Jerina, D.M, Boyer, P.L, Hughes, S.H, Arnold, E. | | Deposit date: | 2002-11-11 | | Release date: | 2003-01-14 | | Last modified: | 2021-10-27 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structures of HIV-1 Reverse Transcriptase with Pre- and Post-translocation AZTMP-terminated DNA
Embo J., 21, 2002
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3TL9
 | | crystal structure of HIV protease model precursor/Saquinavir complex | | Descriptor: | (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide, CHLORIDE ION, GLYCEROL, ... | | Authors: | Agniswamy, J, Sayer, J, Weber, I, Louis, J. | | Deposit date: | 2011-08-29 | | Release date: | 2012-04-25 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.32 Å) | | Cite: | Terminal interface conformations modulate dimer stability prior to amino terminal autoprocessing of HIV-1 protease.
Biochemistry, 51, 2012
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1DXA
 | | BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3'), DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3') | | Authors: | Yeh, H.J.C, Sayer, J.M, Liu, X, Altieri, A.S, Byrd, R.A, Lakshman, M.K, Yagi, H, Schurter, E.J, Gorenstein, D.G, Jerina, D.M. | | Deposit date: | 1995-09-01 | | Release date: | 1995-12-07 | | Last modified: | 2024-03-13 | | Method: | SOLUTION NMR | | Cite: | NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA
Biochemistry, 34, 1995
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1FYY
 | | HPRT GENE MUTATION HOTSPOT WITH A BPDE2(10R) ADDUCT | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, 5'-D(*TP*GP*CP*CP*CP*TP*TP*GP*AP*CP*TP*A)-3', HPRT DNA WITH BENZO[A]PYRENE-ADDUCTED DA7 | | Authors: | Volk, D.E, Rice, J.S, Luxon, B.A, Yeh, H.J.C, Liang, C, Xie, G, Sayer, J.M, Jerina, D.M, Gorenstein, D.G. | | Deposit date: | 2000-10-03 | | Release date: | 2000-12-06 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | NMR evidence for syn-anti interconversion of a trans opened (10R)-dA adduct of benzo[a]pyrene (7S,8R)-diol (9R,10S)-epoxide in a DNA duplex.
Biochemistry, 39, 2000
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2IA6
 | | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, 1,2-ETHANEDIOL, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*A)-3', ... | | Authors: | Bauer, J, Ling, H, Sayer, J.M, Xing, G, Yagi, H, Jerina, D.M. | | Deposit date: | 2006-09-07 | | Release date: | 2007-09-11 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment.
Proc.Natl.Acad.Sci.Usa, 104, 2007
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2IBK
 | | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, 1,2-ETHANEDIOL, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*AP*T)-3', ... | | Authors: | Bauer, J, Ling, H, Sayer, J.M, Xing, G, Yagi, H, Jerina, D.M. | | Deposit date: | 2006-09-11 | | Release date: | 2007-09-11 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment.
Proc.Natl.Acad.Sci.Usa, 104, 2007
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1XO1
 | | T5 5'-EXONUCLEASE MUTANT K83A | | Descriptor: | 5'-EXONUCLEASE | | Authors: | Ceska, T.A, Suck, D, Sayers, J.R. | | Deposit date: | 1998-11-19 | | Release date: | 1999-04-02 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3' exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage.
Proc.Natl.Acad.Sci.USA, 96, 1999
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5HML
 | | Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions | | Descriptor: | 1,2-ETHANEDIOL, 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, ... | | Authors: | Flemming, C.S, Feng, M, Sedelnikova, S.E, Zhang, J, Rafferty, J.B, Sayers, J.R, Artymiuk, P.J. | | Deposit date: | 2016-01-16 | | Release date: | 2016-06-01 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.482 Å) | | Cite: | Direct observation of DNA threading in flap endonuclease complexes.
Nat.Struct.Mol.Biol., 23, 2016
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5HMM
 | | Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Exodeoxyribonuclease, ... | | Authors: | Flemming, C.S, Sedelnikova, S.E, Rafferty, J.B, Sayers, J.R, Artymiuk, P.J. | | Deposit date: | 2016-01-16 | | Release date: | 2016-06-01 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Direct observation of DNA threading in flap endonuclease complexes.
Nat.Struct.Mol.Biol., 23, 2016
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5HP4
 | | Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and metal ions | | Descriptor: | CALCIUM ION, DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3'), Exodeoxyribonuclease, ... | | Authors: | Almalki, F.A, Zhang, J, Sedelnikova, S.E, Rafferty, J.B, Sayers, J.R, Artymiuk, P.A. | | Deposit date: | 2016-01-20 | | Release date: | 2016-06-01 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Direct observation of DNA threading in flap endonuclease complexes.
Nat.Struct.Mol.Biol., 23, 2016
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5HNK
 | | Crystal structure of T5Fen in complex intact substrate and metal ions. | | Descriptor: | DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3'), Exodeoxyribonuclease, GLYCEROL, ... | | Authors: | Almalki, F.A, Feng, M, Zhang, J, Sedelnikova, S.E, Rafferty, J.B, Sayers, J.R, Artymiuk, P.J. | | Deposit date: | 2016-01-18 | | Release date: | 2016-06-01 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2.22 Å) | | Cite: | Direct observation of DNA threading in flap endonuclease complexes.
Nat.Struct.Mol.Biol., 23, 2016
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1EXN
 | | T5 5'-EXONUCLEASE | | Descriptor: | 5'-EXONUCLEASE | | Authors: | Ceska, T.A, Sayers, J.R, Stier, G, Suck, D. | | Deposit date: | 1997-01-17 | | Release date: | 1997-07-07 | | Last modified: | 2018-04-11 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.
Nature, 382, 1996
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