Equivalence class DNA_2.0_20696.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3FL6|1|A+ 3FL6|1|B (rep) | 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3', 5'-D(*CP*GP*CP*AP*CP*GP*C)-3' | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-ray diffraction | 1.17 | 2009-12-29 | ||||
| 2 | 3FL6|1|C+ 3FL6|1|D | 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3', 5'-D(*CP*GP*CP*AP*CP*GP*C)-3' | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-ray diffraction | 1.17 | 2009-12-29 | ||||
| 3 | 1M6R|1|A+ 1M6R|1|B | 5'-R(*G)D(*CP*GP*CP*GP*CP*G)-3' | Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang | X-ray diffraction | 1.54 | 2003-02-25 | ||||
| 4 | 3EYI|1|C+ 3EYI|1|D | 5'-TCGCGCG-3' | The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA | X-ray diffraction | 1.45 | 2009-01-13 | ||||
| 5 | 1MF5|1|A | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT Quadruplex | X-ray diffraction | 1.1 | 2003-02-11 | ||||
| 6 | 1MF5|1|B | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT Quadruplex | X-ray diffraction | 1.1 | 2003-02-11 | ||||
| 7 | 1UB8|1|A+ 1UB8|1|B | 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-ray diffraction | 1.6 | 2004-03-09 | ||||
| 8 | 1UB8|1|C+ 1UB8|1|D | 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-ray diffraction | 1.6 | 2004-03-09 | ||||
| 9 | 1UB8|1|E+ 1UB8|1|F | 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-ray diffraction | 1.6 | 2004-03-09 | ||||
| 10 | 2Z70|1|B | DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DTP*DCP*DGP*DCP*DG)-3') | E.coli RNase 1 in complex with d(CGCGATCGCG) | X-ray diffraction | 1.7 | 2008-06-24 | ||||
| 11 | 2AXY|1|E | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 2005-09-27 | ||||
| 12 | 2AXY|1|F | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 2005-09-27 | ||||
| 13 | 2AXY|1|G | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 2005-09-27 | ||||
| 14 | 2AXY|1|H | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 2005-09-27 | ||||
| 15 | 2PY5|1|D | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 2007-07-17 | ||||
| 16 | 2PY5|1|E | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 2007-07-17 | ||||
| 17 | 2PY5|1|J+ 2PY5|1|Y | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 2007-07-17 | ||||
| 18 | 2PY5|1|L | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 2007-07-17 | ||||
| 19 | 2P2R|1|B | C-rich strand of human telomeric DNA | Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA | X-ray diffraction | 1.6 | 2007-06-12 | ||||
| 20 | 2WBS|1|F+ 2WBS|1|G | 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3', 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3' | Mus musculus | Crystal structure of the zinc finger domain of Klf4 bound to its target DNA | X-ray diffraction | 1.7 | 2010-04-07 | |||
| 21 | 3Q8P|1|P | DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3') | synthetic construct | Human DNA polymerase iota incorporating dCTP opposite 8-oxo-guanine | X-ray diffraction | 1.95 | 2011-02-23 | |||
| 22 | 1SFU|1|C+ 1SFU|1|D | 5'-D(*T*CP*GP*CP*GP*CP*G)-3' | Crystal structure of the viral Zalpha domain bound to left-handed Z-DNA | X-ray diffraction | 2 | 2004-08-17 | ||||
| 23 | 2HEO|1|B+ 2HEO|1|E | 5'-D(*TP*CP*GP*CP*GP*CP*G)-3' | General Structure-Based Approach to the Design of Protein Ligands: Application to the Design of Kv1.2 Potassium Channel Blockers. | X-ray diffraction | 1.7 | 2006-11-21 | ||||
| 24 | 1J75|1|B | 5'-D(*TP*CP*GP*CP*GP*CP*G)-3' | Crystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound to Z-DNA | X-ray diffraction | 1.85 | 2001-09-01 | ||||
| 25 | 1QYL|1|A | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT + Vanadium | X-ray diffraction | 1 | 2003-10-21 | ||||
| 26 | 1QYK|1|A | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT + Barium | X-ray diffraction | 1.4 | 2003-10-21 | ||||
| 27 | 1QYK|1|B | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT + Barium | X-ray diffraction | 1.4 | 2003-10-21 | ||||
| 28 | 1FIU|1|I+ 1FIU|1|J+ 1FIU|1|E+ 1FIU|1|F | DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3'), DNA (5'-D(*TP*GP*CP*G)-3') | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-ray diffraction | 1.6 | 2001-02-07 | ||||
| 29 | 1FIU|1|K+ 1FIU|1|L+ 1FIU|1|G+ 1FIU|1|H | DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3'), DNA (5'-D(*TP*GP*CP*G)-3') | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-ray diffraction | 1.6 | 2001-02-07 | ||||
| 30 | 331D|1|A+ 331D|1|B | DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3') | CRYSTAL STRUCTURE OF D(GCGCGCG) WITH 5'-OVERHANG G'S | X-ray diffraction | 1.65 | 1997-09-24 | ||||
| 31 | 313D|1|A+ 313D|1|B | DNA (5'-D(*GP*(5CM)P*GP*CP*GP*CP*G)-3') | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR | X-ray diffraction | 1.68 | 1997-08-05 | ||||
| 32 | 1PUP|1|A | PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2) | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-ray diffraction | 1.7 | 1997-02-25 | ||||
| 33 | 1PUP|1|B | PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2) | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-ray diffraction | 1.7 | 1997-02-25 | ||||
| 34 | 312D|1|A+ 312D|1|B | DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3'), DNA (5'-D(*CP*CP*GP*CP*GP*CP*G)-3') | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR | X-ray diffraction | 1.8 | 1997-08-28 | ||||
| 35 | 314D|1|A+ 314D|1|B | DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3'), DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3') | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR | X-ray diffraction | 1.9 | 1997-08-05 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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 | 1PUP|1|A | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 1.7 | 7 | NAKB_NA_annotation | NAKB_protein_annotation |
| 2 | 1J75|1|B | Crystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound to Z-DNA | X-RAY DIFFRACTION | 1.85 | 7 | Z-form double helix,double helix,structure | cell cycle,regulatory |
| 3 | 1FIU|1|I+1FIU|1|J+1FIU|1|E+1FIU|1|F | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-RAY DIFFRACTION | 1.6 | 7 | enzyme,hydrolase,nuclease | |
| 4 | 1FIU|1|K+1FIU|1|L+1FIU|1|G+1FIU|1|H | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-RAY DIFFRACTION | 1.6 | 7 | enzyme,hydrolase,nuclease | |
| 5 | 2WBS|1|F+2WBS|1|G | Crystal structure of the zinc finger domain of Klf4 bound to its target DNA | X-RAY DIFFRACTION | 1.7 | 7 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription |
| 6 | 3Q8P|1|P | Human DNA polymerase iota incorporating dCTP opposite 8-oxo-guanine | X-RAY DIFFRACTION | 1.95 | 18 | enzyme,polymerase,transferase | |
| 7 | 1UB8|1|E+1UB8|1|F | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-RAY DIFFRACTION | 1.6 | 7 | double helix,feature,mispair,structure | |
| 8 | 1UB8|1|A+1UB8|1|B | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-RAY DIFFRACTION | 1.6 | 7 | double helix,feature,mispair,structure | |
| 9 | 1UB8|1|C+1UB8|1|D | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-RAY DIFFRACTION | 1.6 | 7 | double helix,feature,mispair,structure | |
| 10 | 2PY5|1|L | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 7 | enzyme,polymerase,transferase | |
| 11 | 3FL6|1|C+3FL6|1|D | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-RAY DIFFRACTION | 1.17 | 7 | B-form double helix,double helix,structure | |
| 12 | 2PY5|1|J+2PY5|1|Y | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 7 | enzyme,polymerase,transferase | |
| 13 | 3FL6|1|A+3FL6|1|B | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-RAY DIFFRACTION | 1.17 | 7 | B-form double helix,double helix,structure | |
| 14 | 2P2R|1|B | Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.6 | 7 | post-transcriptional,regulatory | |
| 15 | 313D|1|A+313D|1|B | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR | X-RAY DIFFRACTION | 1.68 | 7 | Z-form double helix,double helix,structure | |
| 16 | 312D|1|A+312D|1|B | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR | X-RAY DIFFRACTION | 1.8 | 7 | Z-form double helix,double helix,structure | |
| 17 | 2HEO|1|B+2HEO|1|E | General Structure-Based Approach to the Design of Protein Ligands: Application to the Design of Kv1.2 Potassium Channel Blockers. | X-RAY DIFFRACTION | 1.7 | 7 | Z-form double helix,double helix,structure | cell cycle,regulatory |
| 18 | 1SFU|1|C+1SFU|1|D | Crystal structure of the viral Zalpha domain bound to left-handed Z-DNA | X-RAY DIFFRACTION | 2 | 7 | Z-form double helix,double helix,structure | enzyme,hydrolase |
| 19 | 1M6R|1|A+1M6R|1|B | Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang | X-RAY DIFFRACTION | 1.54 | 7 | Z-form double helix,double helix,structure | |
| 20 | 3EYI|1|C+3EYI|1|D | The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA | X-RAY DIFFRACTION | 1.45 | 7 | Z-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead |
| 21 | 331D|1|A+331D|1|B | CRYSTAL STRUCTURE OF D(GCGCGCG) WITH 5'-OVERHANG G'S | X-RAY DIFFRACTION | 1.65 | 7 | Z-form double helix,double helix,structure | |
| 22 | 314D|1|A+314D|1|B | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR | X-RAY DIFFRACTION | 1.9 | 7 | Z-form double helix,double helix,structure | |
| 23 | 2AXY|1|E | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 7 | post-transcriptional,regulatory | |
| 24 | 2AXY|1|H | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 7 | post-transcriptional,regulatory | |
| 25 | 2AXY|1|G | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 7 | post-transcriptional,regulatory | |
| 26 | 2AXY|1|F | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 7 | post-transcriptional,regulatory | |
| 27 | 2PY5|1|E | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 7 | enzyme,polymerase,transferase | |
| 28 | 2PY5|1|D | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 7 | enzyme,polymerase,transferase | |
| 29 | 1MF5|1|A | GCATGCT Quadruplex | X-RAY DIFFRACTION | 1.1 | 7 | quadruplex,structure | |
| 30 | 1QYK|1|B | GCATGCT + Barium | X-RAY DIFFRACTION | 1.4 | 7 | quadruplex,structure | |
| 31 | 1MF5|1|B | GCATGCT Quadruplex | X-RAY DIFFRACTION | 1.1 | 7 | quadruplex,structure | |
| 32 | 1QYK|1|A | GCATGCT + Barium | X-RAY DIFFRACTION | 1.4 | 7 | quadruplex,structure | |
| 33 | 1PUP|1|B | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 1.7 | 7 | NAKB_NA_annotation | NAKB_protein_annotation |
| 34 | 1QYL|1|A | GCATGCT + Vanadium | X-RAY DIFFRACTION | 1 | 7 | quadruplex,structure | |
| 35 | 2Z70|1|B | E.coli RNase 1 in complex with d(CGCGATCGCG) | X-RAY DIFFRACTION | 1.7 | 7 | enzyme,hydrolase,nuclease |
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