Equivalence class DNA_1.5_51692.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1FQ2|1|A+ 1FQ2|1|B (rep) | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | CRYSTAL STRUCTURE ANALYSIS OF THE POTASSIUM FORM OF B-DNA DODECAMER CGCGAATTCGCG | X-ray diffraction | 1.2 | 2000-11-27 | ||||
| 2 | 1N1O|1|A+ 1N1O|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*(TFT)P*TP*CP*GP*CP*G)-3' | Crystal Structure of a B-form DNA Duplex Containing (L)-alpha-threofuranosyl (3'-2') Nucleosides: A Four-Carbon Sugar is Easily Accommodated into the Backbone of DNA | X-ray diffraction | 1.2 | 2002-11-15 | ||||
| 3 | 1DC0|1|A+ 1DC0|1|B | DNA (5'-D(*CP*AP*TP*GP*GP*GP*CP*CP*CP*AP*TP*G)-3') | CRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG | X-ray diffraction | 1.3 | 2000-03-06 | ||||
| 4 | 1DPN|1|A+ 1DPN|1|B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3') | B-DODECAMER CGCGAA(TAF)TCGCG WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE | X-ray diffraction | 0.95 | 2000-04-04 | ||||
| 5 | 2FII|1|A+ 2FII|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UAR)P*CP*GP*CP*G)-3' | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAAT-aU-CGCG, with Incorporated Arabino-Uridin (aU) | X-ray diffraction | 1.24 | 2006-05-23 | ||||
| 6 | 3FDE|1|C+ 3FDE|1|F | 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3', 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3' | Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution | X-ray diffraction | 1.41 | 2009-01-06 | ||||
| 7 | 3FDE|1|D+ 3FDE|1|E | 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3', 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3' | Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution | X-ray diffraction | 1.41 | 2009-01-06 | ||||
| 8 | 3EY3|1|A+ 3EY3|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3' | A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution | X-ray diffraction | 1.25 | 2009-04-28 | ||||
| 9 | 3EY3|1|C+ 3EY3|1|D | 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3' | A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution | X-ray diffraction | 1.25 | 2009-04-28 | ||||
| 10 | 1EI4|1|A+ 1EI4|1|B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TLC)P*(TLC)P*CP*GP*CP*G)-3') | B-DNA DODECAMER CGCGAAT(TLC)CGCG WITH INCORPORATED [3.3.0]BICYCLO-ARABINO-THYMINE-5'-PHOSPHATE | X-ray diffraction | 1.43 | 2000-03-27 | ||||
| 11 | 2FIH|1|A+ 2FIH|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*(UAR)P*TP*CP*GP*CP*G)-3' | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAA-aU-TCGCG, with Incorporated Arabino-Uridine (aU) | X-ray diffraction | 1.13 | 2006-05-23 | ||||
| 12 | 2B3E|1|A+ 2B3E|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | Crystal structure of DB819-D(CGCGAATTCGCG)2 complex. | X-ray diffraction | 1.36 | 2005-11-22 | ||||
| 13 | 455D|1|A+ 455D|1|B | DNA (5'-D(*CP*GP*CP*GP*AP*(SSP)AP*TP*TP*CP*GP*CP*G)-3') | A6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER (CGCGAATTCGCG)2 | X-ray diffraction | 1.43 | 1999-10-08 | ||||
| 14 | 436D|1|A+ 436D|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3' | THE DICKERSON-DREW B-DNA DODECAMER REVISITED-AT ATOMIC RESOLUTION | X-ray diffraction | 1.1 | 1998-11-25 | ||||
| 15 | 2DYW|1|A+ 2DYW|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | A Backbone binding DNA complex | X-ray diffraction | 1.13 | 2007-01-02 | ||||
| 16 | 460D|1|A+ 460D|1|B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3') | A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE | X-ray diffraction | 1.2 | 1999-04-08 | ||||
| 17 | 1JGR|1|A+ 1JGR|1|B | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATTCGCG with Thallium Ions. | X-ray diffraction | 1.2 | 2001-09-05 | ||||
| 18 | 2VLA|1|L+ 2VLA|1|M | 5'-D(*GP*GP*TP*AP*CP*CP*CP*GP*TP*GP *GP*A)-3', 5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP *CP*C)-3' | Crystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNA | X-ray diffraction | 1.3 | 2008-05-06 | ||||
| 19 | 403D|1|A+ 403D|1|B | DNA (5'-D(*CP*GP*CP*(IGU)P*AP*AP*TP*TP*TP*GP*CP*G)-3') | 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE | X-ray diffraction | 1.4 | 1998-07-06 | ||||
| 20 | 355D|1|A+ 355D|1|B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | synthetic construct | THE B-DNA DODECAMER AT HIGH RESOLUTION | X-ray diffraction | 1.4 | 1997-10-13 | |||
| 21 | 2EA0|1|B+ 2EA0|1|C | 5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3', 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate | X-ray diffraction | 1.4 | 2008-02-26 | ||||
| 22 | 463D|1|A+ 463D|1|B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | CALCIUM FORM OF D(CGCGAATTCGCG)2 | X-ray diffraction | 1.45 | 1999-10-08 | ||||
| 23 | 2DPB|1|A+ 2DPB|1|B | DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3') | Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine | X-ray diffraction | 1.5 | 2007-04-17 | ||||
| 24 | 461D|1|A+ 461D|1|B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3') | A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE | X-ray diffraction | 1.5 | 1999-04-08 | ||||
| 25 | 3JXY|1|B+ 3JXY|1|C | DNA (5'-D(*CP*GP*GP*AP*CP*TP*GP*AP*CP*GP*GP*G)-3'), DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3') | Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing a GT Mismatch | X-ray diffraction | 1.5 | 2010-09-22 |
Release history
| Release | 0.19 |
|---|---|
| Date | 2011-05-28 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length | NAKB_NA_annotation | NAKB_protein_annotation |
|---|---|---|---|---|---|---|---|
| 1 | 3FDE|1|C+3FDE|1|F | Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution | X-RAY DIFFRACTION | 1.41 | 12 | B-form double helix,double helix,structure | enzyme,ligase |
| 2 | 3FDE|1|D+3FDE|1|E | Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution | X-RAY DIFFRACTION | 1.41 | 12 | B-form double helix,double helix,structure | enzyme,ligase |
| 3 | 463D|1|A+463D|1|B | CALCIUM FORM OF D(CGCGAATTCGCG)2 | X-RAY DIFFRACTION | 1.45 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 4 | 1DPN|1|A+1DPN|1|B | B-DODECAMER CGCGAA(TAF)TCGCG WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE | X-RAY DIFFRACTION | 0.95 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 5 | 2DPB|1|A+2DPB|1|B | Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine | X-RAY DIFFRACTION | 1.5 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 6 | 1EI4|1|A+1EI4|1|B | B-DNA DODECAMER CGCGAAT(TLC)CGCG WITH INCORPORATED [3.3.0]BICYCLO-ARABINO-THYMINE-5'-PHOSPHATE | X-RAY DIFFRACTION | 1.43 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 7 | 403D|1|A+403D|1|B | 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE | X-RAY DIFFRACTION | 1.4 | 12 | B-form double helix,double helix,structure | |
| 8 | 1JGR|1|A+1JGR|1|B | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATTCGCG with Thallium Ions. | X-RAY DIFFRACTION | 1.2 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 9 | 1FQ2|1|A+1FQ2|1|B | CRYSTAL STRUCTURE ANALYSIS OF THE POTASSIUM FORM OF B-DNA DODECAMER CGCGAATTCGCG | X-RAY DIFFRACTION | 1.2 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 10 | 355D|1|A+355D|1|B | THE B-DNA DODECAMER AT HIGH RESOLUTION | X-RAY DIFFRACTION | 1.4 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 11 | 1N1O|1|A+1N1O|1|B | Crystal Structure of a B-form DNA Duplex Containing (L)-alpha-threofuranosyl (3'-2') Nucleosides: A Four-Carbon Sugar is Easily Accommodated into the Backbone of DNA | X-RAY DIFFRACTION | 1.2 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 12 | 2FIH|1|A+2FIH|1|B | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAA-aU-TCGCG, with Incorporated Arabino-Uridine (aU) | X-RAY DIFFRACTION | 1.13 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 13 | 2FII|1|A+2FII|1|B | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAAT-aU-CGCG, with Incorporated Arabino-Uridin (aU) | X-RAY DIFFRACTION | 1.24 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 14 | 461D|1|A+461D|1|B | A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE | X-RAY DIFFRACTION | 1.5 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 15 | 460D|1|A+460D|1|B | A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE | X-RAY DIFFRACTION | 1.2 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 16 | 436D|1|A+436D|1|B | THE DICKERSON-DREW B-DNA DODECAMER REVISITED-AT ATOMIC RESOLUTION | X-RAY DIFFRACTION | 1.1 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 17 | 2B3E|1|A+2B3E|1|B | Crystal structure of DB819-D(CGCGAATTCGCG)2 complex. | X-RAY DIFFRACTION | 1.36 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 18 | 455D|1|A+455D|1|B | A6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER (CGCGAATTCGCG)2 | X-RAY DIFFRACTION | 1.43 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 19 | 2DYW|1|A+2DYW|1|B | A Backbone binding DNA complex | X-RAY DIFFRACTION | 1.13 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 20 | 3EY3|1|C+3EY3|1|D | A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution | X-RAY DIFFRACTION | 1.25 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 21 | 3EY3|1|A+3EY3|1|B | A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution | X-RAY DIFFRACTION | 1.25 | 12 | B-form double helix,DNA dodecamer,double helix,feature,structure | |
| 22 | 2VLA|1|L+2VLA|1|M | Crystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNA | X-RAY DIFFRACTION | 1.3 | 12 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 23 | 3JXY|1|B+3JXY|1|C | Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing a GT Mismatch | X-RAY DIFFRACTION | 1.5 | 12 | double helix,feature,mispair,structure | enzyme,hydrolase |
| 24 | 2EA0|1|B+2EA0|1|C | Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate | X-RAY DIFFRACTION | 1.4 | 12 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease |
| 25 | 1DC0|1|A+1DC0|1|B | CRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG | X-RAY DIFFRACTION | 1.3 | 12 | A-form double helix,double helix,structure |
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