Dual Topology: 3_4
![](../biomath/rag/dual_images2019/3_4.png)
Topological Aspects
- 3 Vertices
- Eigenvalues
- 0.0000000000
- 2.0000000000
- 6.0000000000
Examples of actual RNAs corresponding to this structure from RNA databases: 176
PDB_Chain | Type | Discovery Method |
---|---|---|
1A9L_A | PRE-TRNA BULGE-HELIX-BULGE MOTIF | SOLUTION NMR |
1CQ5_A | SRP RNA DOMAIN IV | SOLUTION NMR |
1CQL_A | SRP DOMAIN IV RNA | SOLUTION NMR |
1DUL_B | 4.5 S RNA DOMAIN IV | X-RAY DIFFRACTION |
1DZ5_CD | PIE, RNA (5'-R(*GP*AP*GP*AP*CP*AP*UP*UP*GP*CP*AP*C | SOLUTION NMR |
1EHT_A | THEOPHYLLINE-BINDING RNA | SOLUTION NMR |
1EXY_A | RNA APTAMER, 33-MER | SOLUTION NMR |
1F1T_A | MALACHITE GREEN APTAMER RNA | X-RAY DIFFRACTION |
1FUF_AB | (5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P* | X-RAY DIFFRACTION |
1HQ1_B | 4.5S RNA DOMAIN IV | X-RAY DIFFRACTION |
1J7T_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
1JU1_AB | HIV-1Lai SL1 | SOLUTION NMR |
1LC4_AB | 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP | X-RAY DIFFRACTION |
1M5L_A | modified HIV-1 packaging signal stem-loop 1 RNA | SOLUTION NMR |
1MWL_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
1MZP_B | fragment of 23S rRNA | X-RAY DIFFRACTION |
1NBK_A | RNA aptamer | SOLUTION NMR |
1NLC_BA | HIV-1 DIS(MAL) genomic RNA | X-RAY DIFFRACTION |
1NTA_AB | 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP | X-RAY DIFFRACTION |
1NTB_AB | 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP | X-RAY DIFFRACTION |
1O15_A | THEOPHYLLINE-BINDING RNA | SOLUTION NMR |
1O3Z_BA | HIV-1 DIS(MAL) GENOMIC RNA | X-RAY DIFFRACTION |
1O9M_AB | EUBACTERIAL A-SITE | X-RAY DIFFRACTION |
1P5M_A | 55-MER | SOLUTION NMR |
1Q8N_A | RNA Aptamer | SOLUTION NMR |
1TXS_A | Enteroviral 5'-UTR | SOLUTION NMR |
1U3K_A | ABISS7 | SOLUTION NMR |
1ULL_A | RNA (5'-R (GP*GP*CP*UP*GP*GP*AP*CP*UP*CP*GP*UP*AP* | SOLUTION NMR |
1WVD_BA | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP | X-RAY DIFFRACTION |
1Y6S_BA | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP | X-RAY DIFFRACTION |
1Y6T_BA | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP | X-RAY DIFFRACTION |
1Y73_BA | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP | X-RAY DIFFRACTION |
1Y90_BA | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP | X-RAY DIFFRACTION |
1Y95_BA | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP | X-RAY DIFFRACTION |
1Y99_AB | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP | X-RAY DIFFRACTION |
1YRJ_AB | Bacterial 16 S Ribosomal RNA A Site Oligonucleotid | X-RAY DIFFRACTION |
2A9L_A | ABISS7 RNA | SOLUTION NMR |
2BE0_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
2BEE_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
2D18_AB | 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP | SOLUTION NMR |
2ESI_AB | 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP | X-RAY DIFFRACTION |
2ESJ_AB | 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP | X-RAY DIFFRACTION |
2ET3_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
2ET4_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
2ET5_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
2ET8_AB | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP | X-RAY DIFFRACTION |
2F4S_AB | 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*A | X-RAY DIFFRACTION |
2F4T_BA | 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*A | X-RAY DIFFRACTION |
2F4U_AB | 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*A | X-RAY DIFFRACTION |
2FEY_A | stem-loop IV of Tetrahymena telomerase RNA | SOLUTION NMR |
2FQN_AB | 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP | X-RAY DIFFRACTION |
2G5K_AB | 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP | X-RAY DIFFRACTION |
2HUA_A | CSFV IRES Domain IIa | SOLUTION NMR |
2KTZ_A | HCV IRES Domain IIa RNA | SOLUTION NMR |
2KU0_A | HCV IRES Domain IIa RNA | SOLUTION NMR |
2KX8_A | 7SK | SOLUTION NMR |
2KZL_A | RNA (55-MER) | SOLUTION NMR |
2M57_A | RNA_(35-MER) | SOLUTION NMR |
2MQT_A | RNA (68-MER) | SOLUTION NMR |
2MQV_B | RNA (68-MER) | SOLUTION NMR |
2N6T_A | RNA (42-MER) | SOLUTION NMR |
2N6W_A | RNA (68-MER) | SOLUTION NMR |
2O3V_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP* | X-RAY DIFFRACTION |
2O3W_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP* | X-RAY DIFFRACTION |
2O3X_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP* | X-RAY DIFFRACTION |
2O3Y_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP* | X-RAY DIFFRACTION |
2OIJ_AB | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP | X-RAY DIFFRACTION |
2OIY_AB | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP | X-RAY DIFFRACTION |
2OJ0_AB | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP | X-RAY DIFFRACTION |
2PN3_AB | 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP | X-RAY DIFFRACTION |
2PWT_AB | 22-mer of the ribosomal decoding site | X-RAY DIFFRACTION |
2PXB_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXD_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXE_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXF_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXK_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXL_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXP_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXQ_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXT_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXU_B | 4.5 S RNA | X-RAY DIFFRACTION |
2PXV_B | 4.5 S RNA | X-RAY DIFFRACTION |
2QEK_AB | HIV-1 subtype F DIS genomic RNA | X-RAY DIFFRACTION |
2XKV_B | 4.5S RNA | ELECTRON MICROSCOPY |
357D_CBA | RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP* | X-RAY DIFFRACTION |
364D_CBA | RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP* | X-RAY DIFFRACTION |
3BNL_AB | A site of bacterial ribosome | X-RAY DIFFRACTION |
3BNP_AB | A site of bacterial ribosome | X-RAY DIFFRACTION |
3C44_AB | HIV-1 subtype F genomic RNA | X-RAY DIFFRACTION |
3DVV_AB | HIV-1 genomic RNA | X-RAY DIFFRACTION |
3FAR_AB | RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP* | X-RAY DIFFRACTION |
3LOA_BA | 5'-R(*CP*CP*GP*CP*GP*CP*CP*CP*GP*(5BU)P*CP*AP*CP*A | X-RAY DIFFRACTION |
3LQX_B | SRP RNA | X-RAY DIFFRACTION |
3S4P_AB | RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP | X-RAY DIFFRACTION |
3TD0_BA | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP | X-RAY DIFFRACTION |
3TD1_BA | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP | X-RAY DIFFRACTION |
3TZR_AB | 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP | X-RAY DIFFRACTION |
3WBM_XY | RNA (25-MER) | X-RAY DIFFRACTION |
3WRU_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP* | X-RAY DIFFRACTION |
3ZN8_G | 4.5 S RNA | ELECTRON MICROSCOPY |
462D_BA | RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP* | X-RAY DIFFRACTION |
4F8U_AB | RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP | X-RAY DIFFRACTION |
4F8V_AB | RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP | X-RAY DIFFRACTION |
4GPW_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP* | X-RAY DIFFRACTION |
4GPX_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP* | X-RAY DIFFRACTION |
4GPY_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP* | X-RAY DIFFRACTION |
4K31_BC | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP* | X-RAY DIFFRACTION |
4K32_AB | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP* | X-RAY DIFFRACTION |
4P20_AB | 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP | X-RAY DIFFRACTION |
4P3S_BA | 5'-D(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*A | X-RAY DIFFRACTION |
4P3T_AB | 5'-D(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*A | X-RAY DIFFRACTION |
4PDB_I | SELEX RNA aptamer | X-RAY DIFFRACTION |
4PDQ_AB | RNA (5'-*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP | X-RAY DIFFRACTION |
4PHY_AB | RNA (26-MER) | X-RAY DIFFRACTION |
4PMI_A | Rev-Response-Element RNA | X-RAY DIFFRACTION |
5EW4_BA | RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP* | X-RAY DIFFRACTION |
5EW7_BA | RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP* | X-RAY DIFFRACTION |
5M0H_A | ASH1 E3 (42 NT-TL/TLR) | X-RAY DIFFRACTION |
5OB3_A | RNA aptamer (69-MER) | X-RAY DIFFRACTION |
5VT0_R | ESCHERICHIA COLI 6S RNA DERIVATIVE (112-MER) | ELECTRON MICROSCOPY |
5ZEI_AB | RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*G | X-RAY DIFFRACTION |
5ZEJ_AB | RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*G | X-RAY DIFFRACTION |
5ZEM_AB | RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*G | X-RAY DIFFRACTION |
6CF2_G | RNA (35-MER) | X-RAY DIFFRACTION |
1QZW_F | 7S RNA | X-RAY DIFFRACTION |
1R3E_DE | 5'-R(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*A | X-RAY DIFFRACTION |
1RY1_NM | RNA (31-MER) | ELECTRON MICROSCOPY |
2GJW_IJL | 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP | X-RAY DIFFRACTION |
2NOK_CD | 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP | X-RAY DIFFRACTION |
2NOQ_DC | 18S ribosomal RNA | ELECTRON MICROSCOPY |
2NOQ_E | 25S RIBOSOMAL RNA | ELECTRON MICROSCOPY |
2OM7_H | Fragment of23S rRNA (H89) | ELECTRON MICROSCOPY |
2OM7_I | FRAGMENT OF23S RRNA (H42-44) | ELECTRON MICROSCOPY |
2OM7_J | Fragment of23S rRNA (H76) | ELECTRON MICROSCOPY |
2PN4_AB | 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP | X-RAY DIFFRACTION |
2WW9_D | 25S RRNA | ELECTRON MICROSCOPY |
2WWA_D | 25S RRNA | ELECTRON MICROSCOPY |
3BNN_CD | A site of human ribosome | X-RAY DIFFRACTION |
3BNO_AB | A site of human mitochondrial ribosome | X-RAY DIFFRACTION |
3BNQ_AB | A site of human mitochondrial ribosome | X-RAY DIFFRACTION |
3BNR_AB | A site of human mitochondrial ribosome | X-RAY DIFFRACTION |
3BNS_AB | A site of human mitochondrial ribosome | X-RAY DIFFRACTION |
3J0D_hH | ribosomal 16S RNA | ELECTRON MICROSCOPY |
3J0E_eE | ribosomal 16S RNA | ELECTRON MICROSCOPY |
3J0L_7 | 60S RIBOSOMAL RNA FRAGMENT | ELECTRON MICROSCOPY |
3J0L_1 | 60S RIBOSOMAL RNA FRAGMENT | ELECTRON MICROSCOPY |
3J0O_7 | 60S ribosomal RNA fragment | ELECTRON MICROSCOPY |
3J0P_7 | 60S RIBOSOMAL RNA FRAGMENT | ELECTRON MICROSCOPY |
3J0Q_7 | 60S RIBOSOMAL RNA FRAGMENT | ELECTRON MICROSCOPY |
3J46_4 | 23S ribosomal RNA | ELECTRON MICROSCOPY |
3JCM_E | SNR14 SNRNA | ELECTRON MICROSCOPY |
4CXG_2 | 28S RRNA - H89 | ELECTRON MICROSCOPY |
4CXH_2 | 28S RRNA - H89 | ELECTRON MICROSCOPY |
4JRC_B | Distal Stem I region of the glyQS T box leader RNA | X-RAY DIFFRACTION |
4WCE_Y | 5S RRNA | X-RAY DIFFRACTION |
4WFA_Y | 5S RRNA | X-RAY DIFFRACTION |
4WFB_Y | 5S RRNA | X-RAY DIFFRACTION |
4ZC7_AB | RNA duplex | X-RAY DIFFRACTION |
5BTM_A | RNA (55-mer) | X-RAY DIFFRACTION |
5BWS_AB | RNA (5'-D(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP* | X-RAY DIFFRACTION |
5BXK_CD | RNA (5'-D(P*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP | X-RAY DIFFRACTION |
5FJ0_AB | HMKT-7 | X-RAY DIFFRACTION |
5G4U_IJ | HMKT-7 | X-RAY DIFFRACTION |
5G4V_AB | HMKT-7 | X-RAY DIFFRACTION |
5GAD_1 | ESRP 4.5S RNA | ELECTRON MICROSCOPY |
5GAF_1 | SRP 4.5S RNA | ELECTRON MICROSCOPY |
5GAG_1 | SRP 4.5S RNA | ELECTRON MICROSCOPY |
5GAH_1 | SRP 4.5S RNA | ELECTRON MICROSCOPY |
5HKV_Y | 5S RIBOSOMAL RNA | X-RAY DIFFRACTION |
5HL7_Y | 5S RIBOSOMAL RNA | X-RAY DIFFRACTION |
5NRG_Y | 5S RIBOSOMAL RNA | X-RAY DIFFRACTION |
5T7V_C | 5S ribosomal RNA | ELECTRON MICROSCOPY |
5TF6_B | U6 snRNA | X-RAY DIFFRACTION |
5V1L_CD | RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G) | X-RAY DIFFRACTION |
5XZ1_AB | RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP* | X-RAY DIFFRACTION |
5Y7M_D | RNA (52-MER) | X-RAY DIFFRACTION |