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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Lu, J.X."

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Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Saccharolobus solfataricus P2 (3)
	synthetic construct (3)
	Saccharomyces cerevisiae S288C (2)
	Geobacillus stearothermophilus (1)

Taxonomy

	Archaea (3)
	other sequences (3)
	Eukaryota (2)
	Bacteria (1)

Experimental Method

	SOLUTION NMR (7)
	X-RAY DIFFRACTION (6)

Polymer Entity Type

	DNA (13)
	Protein (6)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (1)
	2.5 - 3.0 (2)

Release Date

	1995 - 1999 (5)
	2000 - 2004 (3)
	2005 - 2009 (3)
	2015 - 2019 (2)

Enzyme Classification Name

Transferases (6)

Symmetry Type

Asymmetric (6)

SCOP Classification

	Multi-domain proteins (alpha and beta) (4)
	Alpha and beta proteins (a+b) (3)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 13 of 13 Structures

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1AXL \| pdb_00001axl	Download File View File

SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES

Feng, B., Gorin, A.A., Kolbanovskiy, A., Hingerty, B.E., Geacintov, N.E., Broyde, S., Patel, D.J.

(1997) Biochemistry 36: 13780-13790

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG) (nucleic acid)
Unique Ligands	BAP

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1AXO \| pdb_00001axo	Download File View File

STRUCTURAL ALIGNMENT OF THE (+)-TRANS-ANTI-[BP]DG ADDUCT POSITIONED OPPOSITE DC AT A DNA TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES

Feng, B., Gorin, A.A., Hingerty, B.E., Geacintov, N.E., Broyde, S., Patel, D.J.

(1997) Biochemistry 36: 13769-13779

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(AAC-[BP]G-CTACCATCC)D(GGATGGTAGC) (nucleic acid)
Unique Ligands	BAP

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1AXV \| pdb_00001axv	Download File View File

SOLUTION NMR STRUCTURE OF THE [BP]DA ADDUCT OPPOSITE DT IN A DNA DUPLEX, 6 STRUCTURES

Mao, B., Gu, Z., Gorin, A.A., Chen, J., Hingerty, B.E., Amid, S., Broyde, S., Geacintov, N.E., Patel, D.J.

(1999) Biochemistry 38: 10831-10842

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(CTCTC-[BP]A-CTTCC)D(GGAAGTGAGAG) (nucleic acid)
Unique Ligands	BAP

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1BPS \| pdb_00001bps	Download File View File

MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

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.

(1997) Biochemistry 36: 11069-11076

Released	1998-08-19
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	DNA (5'-D(CPTPCPGPGPGPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPCP(BAP)APCPGPAPG)-3') (nucleic acid)
Unique Ligands	BAP

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1DXA \| pdb_00001dxa	Download File View File

BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

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.

(1995) Biochemistry 34: 13570-13581

Released	1995-12-07
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPTPCPGPGPGPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPCPAPCPGPAPG)-3') (nucleic acid)
Unique Ligands	BAP

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1FYY \| pdb_00001fyy	Download File View File

HPRT GENE MUTATION HOTSPOT WITH A BPDE2(10R) ADDUCT

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.

(2000) Biochemistry 39: 14040-14053

Released	2000-12-06
Method	SOLUTION NMR
Macromolecule	5'-D(TPGPCPCPCPTPTPGPAPCPTPA)-3' (nucleic acid) HPRT DNA WITH BENZO[A]PYRENE-ADDUCTED DA7 (nucleic acid)
Unique Ligands	BAP

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1S0M \| pdb_00001s0m	Download File View File

Crystal structure of a Benzo[a]pyrene Diol Epoxide adduct in a ternary complex with a DNA polymerase

Ling, H., Sayer, J.M., Boudsocq, F., Plosky, B.S., Woodgate, R., Yang, W.

(2004) Proc Natl Acad Sci U S A 101: 2265-2269

Released	2004-03-30
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPT)-3' (nucleic acid) 5'-D(PAPTPAPAPAPTPCPCPTPTPCPCPCPCPCP*A)-3' (nucleic acid)
Unique Ligands	BAP, CA, DTP, MG

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1XC9 \| pdb_00001xc9	Download File View File

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

Hsu, G.W., Huang, X., Luneva, N.P., Geacintov, N.E., Beese, L.S.

(2005) J Biological Chem 280: 3764-3770

Released	2004-12-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA polymerase I (protein) DNA primer strand (nucleic acid) DNA template strand with benzo[a]pyrene adduct (nucleic acid)
Unique Ligands	BAP, MG, SO4
Unique branched monosaccharides	FRU, GLC

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1Y9H \| pdb_00001y9h	Download File View File

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement

Zhang, N., Lin, C., Huang, X., Kolbanovskiy, A., Hingerty, B.E., Amin, S., Broyde, S., Geacintov, N.E., Patel, D.J.

(2005) J Mol Biology 346: 951-965

Released	2005-03-22
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPAPTP(5CM)P(BPG)PCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPCPGPAPTPGPG)-3' (nucleic acid)
Unique Ligands	BAP

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2IA6 \| pdb_00002ia6	Download File View File

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.

(2007) Proc Natl Acad Sci U S A 104: 14905-14910

Released	2007-09-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPA)-3' (nucleic acid) 5'-D(TPCPAPTPGPAPAPTPCPCPTPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	ATP, BAP, CA, EDO, GOL, PO4

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2IBK \| pdb_00002ibk	Download File View File

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.

(2007) Proc Natl Acad Sci U S A 104: 14905-14910

Released	2007-09-11
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPAPT)-3' (nucleic acid) 5'-D(TPCPAPTPGPAPAPTPCPCPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	BAP, CA, EDO, GOL, POP

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5WM1 \| pdb_00005wm1	Download File View File

Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex

Rechkoblit, O., Kolbanovsky, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.

(2017) Nat Commun 8: 965-965

Released	2017-10-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	DNA repair protein REV1 (protein) DNA (5'-D(GPGPGPGPTPGPTPGPGPTPAP(DDG))-3') (nucleic acid) DNA (5'-D(PAPTPCPGPCPTPAPCPCPAPCPAPCPCPCPC)-3') (nucleic acid)
Unique Ligands	BAP, DCP, EDO, GOL, MG, PEG

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5WM8 \| pdb_00005wm8	Download File View File

Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex

Rechkoblit, O., Kolbanovsky, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.

(2017) Nat Commun 8: 965-965

Released	2017-10-25
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	DNA repair protein REV1 (protein) DNA (5'-D(GPGPGPGPTPGPTPGPGPTPAP(DDG))-3') (nucleic acid) DNA (5'-D(PAPTPCPGPCPTPAPCPCPAPCPAPCPCPCPC)-3') (nucleic acid)
Unique Ligands	BAP, DCP, EDO, GOL, MG, PEG

1 to 13 of 13 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1AXL | pdb_00001axl

SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES

1AXO | pdb_00001axo

STRUCTURAL ALIGNMENT OF THE (+)-TRANS-ANTI-[BP]DG ADDUCT POSITIONED OPPOSITE DC AT A DNA TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES

1AXV | pdb_00001axv

SOLUTION NMR STRUCTURE OF THE [BP]DA ADDUCT OPPOSITE DT IN A DNA DUPLEX, 6 STRUCTURES

1BPS | pdb_00001bps

MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

1DXA | pdb_00001dxa

BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

1FYY | pdb_00001fyy

HPRT GENE MUTATION HOTSPOT WITH A BPDE2(10R) ADDUCT

1S0M | pdb_00001s0m

Crystal structure of a Benzo[a]pyrene Diol Epoxide adduct in a ternary complex with a DNA polymerase

1XC9 | pdb_00001xc9

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

1Y9H | pdb_00001y9h

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement

2IA6 | pdb_00002ia6

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

2IBK | pdb_00002ibk

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

5WM1 | pdb_00005wm1

Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex

5WM8 | pdb_00005wm8

Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1AXL | pdb_00001axl

1AXO | pdb_00001axo

1AXV | pdb_00001axv

1BPS | pdb_00001bps

1DXA | pdb_00001dxa

1FYY | pdb_00001fyy

1S0M | pdb_00001s0m

1XC9 | pdb_00001xc9

1Y9H | pdb_00001y9h

2IA6 | pdb_00002ia6

2IBK | pdb_00002ibk

5WM1 | pdb_00005wm1

5WM8 | pdb_00005wm8