Complex 6ymi
System information
| Experimental technique | X-ray |
| Experimental resolution | 2.50 |
| System mass | 72.85 kDa |
| Deposition year | 2020 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Roseobacter |
| RCSB PDB Entry | 6ymi |
| Reference | Huang Lin, Liao Ting-Wei, Wang Jia, Ha Taekjip, Lilley David M J. . Crystal structure and ligand-induced folding of the SAM/SAH riboswitch Nucleic Acids Research |
| Equivalence Class |
NR_all_57046.3
BGSU version: 4.49 |
| Compound | AMP |
| Residue | . / 101 |
| Chain | T / G |
| Non-redundant | False |
| Interacting RNA chains | E/F, F/G |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | E/F: riboswitch, F/G: riboswitch |
| RNA family global | riboswitch |
| Volume | 73.75 Å3 |
| Hydrophobicity | 0.246 |
| Hydrophilicity | 0.839 |
| Buriedness | 0.533 |
| Don/acc character | 4.957 |
| SiteScore | 0.733 |
| D Score | 0.543 |
| Kd | — |
| Compound | AMP |
| Residue | . / 102 |
| Chain | N / A |
| Non-redundant | False |
| Interacting RNA chains | B/B, A/A |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: riboswitch, B/B: riboswitch |
| RNA family global | riboswitch |
| Volume | 66.89 Å3 |
| Hydrophobicity | 0.312 |
| Hydrophilicity | 1.015 |
| Buriedness | 0.571 |
| Don/acc character | 2.370 |
| SiteScore | 0.732 |
| D Score | 0.518 |
| Kd | — |
| Compound | AMP |
| Residue | . / 103 |
| Chain | O / A |
| Non-redundant | False |
| Interacting RNA chains | B/B, A/A |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: riboswitch, B/B: riboswitch |
| RNA family global | riboswitch |
| Volume | 382.10 Å3 |
| Hydrophobicity | 0.239 |
| Hydrophilicity | 1.064 |
| Buriedness | 0.685 |
| Don/acc character | 2.059 |
| SiteScore | 1.141 |
| D Score | 1.004 |
| Kd | — |
| Compound | AMP |
| Residue | . / 102 |
| Chain | Q / C |
| Non-redundant | False |
| Interacting RNA chains | C/C, D/D |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: riboswitch, D/D: riboswitch |
| RNA family global | riboswitch |
| Volume | 454.13 Å3 |
| Hydrophobicity | 0.425 |
| Hydrophilicity | 1.039 |
| Buriedness | 0.677 |
| Don/acc character | 1.812 |
| SiteScore | 1.137 |
| D Score | 1.008 |
| Kd | — |
| Compound | AMP |
| Residue | . / 102 |
| Chain | S / F |
| Non-redundant | False |
| Interacting RNA chains | E/F, F/G |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | E/F: riboswitch, F/G: riboswitch |
| RNA family global | riboswitch |
| Volume | 405.08 Å3 |
| Hydrophobicity | 0.275 |
| Hydrophilicity | 0.991 |
| Buriedness | 0.666 |
| Don/acc character | 1.942 |
| SiteScore | 1.138 |
| D Score | 1.017 |
| Kd | — |
| Compound | AMP |
| Residue | . / 102 |
| Chain | V / I |
| Non-redundant | False |
| Interacting RNA chains | G/I, H/J |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | G/I: riboswitch, H/J: riboswitch |
| RNA family global | riboswitch |
| Volume | 394.79 Å3 |
| Hydrophobicity | 0.429 |
| Hydrophilicity | 1.030 |
| Buriedness | 0.720 |
| Don/acc character | 1.639 |
| SiteScore | 1.167 |
| D Score | 1.037 |
| Kd | — |
| Compound | AMP |
| Residue | . / 102 |
| Chain | X / M |
| Non-redundant | False |
| Interacting RNA chains | J/N, I/M |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | I/M: riboswitch, J/N: riboswitch |
| RNA family global | riboswitch |
| Volume | 385.19 Å3 |
| Hydrophobicity | 0.229 |
| Hydrophilicity | 1.033 |
| Buriedness | 0.649 |
| Don/acc character | 2.012 |
| SiteScore | 1.119 |
| D Score | 0.993 |
| Kd | — |
| Compound | AMP |
| Residue | . / 101 |
| Chain | Y / N |
| Non-redundant | False |
| Interacting RNA chains | J/N, I/M |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | I/M: riboswitch, J/N: riboswitch |
| RNA family global | riboswitch |
| Volume | 65.51 Å3 |
| Hydrophobicity | 0.282 |
| Hydrophilicity | 0.986 |
| Buriedness | 0.567 |
| Don/acc character | 4.212 |
| SiteScore | 0.676 |
| D Score | 0.449 |
| Kd | — |
| Compound | AMP |
| Residue | . / 201 |
| Chain | Z / O |
| Non-redundant | False |
| Interacting RNA chains | L/P, K/O |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | K/O: riboswitch, L/P: riboswitch |
| RNA family global | riboswitch |
| Volume | 398.91 Å3 |
| Hydrophobicity | 0.339 |
| Hydrophilicity | 1.030 |
| Buriedness | 0.668 |
| Don/acc character | 1.565 |
| SiteScore | 1.132 |
| D Score | 1.005 |
| Kd | — |
| Compound | CBV |
| Residue | . / 101 |
| Chain | P / C |
| Non-redundant | True |
| Interacting RNA chains | C/C |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: riboswitch |
| RNA family global | riboswitch |
| Volume | 32.59 Å3 |
| Hydrophobicity | 0.330 |
| Hydrophilicity | 0.898 |
| Buriedness | 0.566 |
| Don/acc character | 0.767 |
| SiteScore | 0.684 |
| D Score | 0.467 |
| Kd | — |
| Compound | CBV |
| Residue | . / 101 |
| Chain | U / I |
| Non-redundant | True |
| Interacting RNA chains | G/I |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | G/I: riboswitch |
| RNA family global | riboswitch |
| Volume | 33.96 Å3 |
| Hydrophobicity | 0.327 |
| Hydrophilicity | 0.850 |
| Buriedness | 0.580 |
| Don/acc character | 0.679 |
| SiteScore | 0.595 |
| D Score | 0.353 |
| Kd | — |