Complex 6ymk
System information
| Experimental technique | X-ray |
| Experimental resolution | 2.03 |
| System mass | 70.63 kDa |
| Deposition year | 2020 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Roseobacter |
| RCSB PDB Entry | 6ymk |
| 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: 4.48 |
| Compound | MTA |
| Residue | . / 101 |
| Chain | M / 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 | 394.45 Å3 |
| Hydrophobicity | 0.412 |
| Hydrophilicity | 1.054 |
| Buriedness | 0.679 |
| Don/acc character | 1.636 |
| SiteScore | 1.138 |
| D Score | 1.004 |
| Kd | — |
| Compound | MTA |
| Residue | . / 101 |
| Chain | N / B |
| 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 | 80.26 Å3 |
| Hydrophobicity | 0.408 |
| Hydrophilicity | 1.006 |
| Buriedness | 0.607 |
| Don/acc character | 2.437 |
| SiteScore | 0.777 |
| D Score | 0.568 |
| Kd | — |
| Compound | MTA |
| Residue | . / 101 |
| Chain | O / C |
| Non-redundant | False |
| Interacting RNA chains | D/D, C/C |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: riboswitch, D/D: riboswitch |
| RNA family global | riboswitch |
| Volume | 425.66 Å3 |
| Hydrophobicity | 0.424 |
| Hydrophilicity | 0.975 |
| Buriedness | 0.669 |
| Don/acc character | 1.600 |
| SiteScore | 1.143 |
| D Score | 1.023 |
| Kd | — |
| Compound | MTA |
| Residue | . / 101 |
| Chain | R / F |
| Non-redundant | False |
| Interacting RNA chains | F/G, E/F |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | E/F: riboswitch, F/G: riboswitch |
| RNA family global | riboswitch |
| Volume | 433.21 Å3 |
| Hydrophobicity | 0.336 |
| Hydrophilicity | 0.992 |
| Buriedness | 0.654 |
| Don/acc character | 1.536 |
| SiteScore | 1.130 |
| D Score | 1.009 |
| Kd | — |
| Compound | MTA |
| Residue | . / 101 |
| Chain | T / G |
| Non-redundant | False |
| Interacting RNA chains | F/G, E/F |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | E/F: riboswitch, F/G: riboswitch |
| RNA family global | riboswitch |
| Volume | 88.15 Å3 |
| Hydrophobicity | 0.399 |
| Hydrophilicity | 0.962 |
| Buriedness | 0.575 |
| Don/acc character | 1.976 |
| SiteScore | 0.771 |
| D Score | 0.571 |
| Kd | — |
| Compound | MTA |
| Residue | . / 101 |
| Chain | U / 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 | 340.60 Å3 |
| Hydrophobicity | 0.357 |
| Hydrophilicity | 1.033 |
| Buriedness | 0.717 |
| Don/acc character | 1.620 |
| SiteScore | 1.164 |
| D Score | 1.033 |
| Kd | — |
| Compound | MTA |
| Residue | . / 101 |
| Chain | W / 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 | 90.21 Å3 |
| Hydrophobicity | 0.337 |
| Hydrophilicity | 0.932 |
| Buriedness | 0.580 |
| Don/acc character | 1.625 |
| SiteScore | 0.780 |
| D Score | 0.584 |
| Kd | — |
| Compound | MTA |
| 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 | 351.58 Å3 |
| Hydrophobicity | 0.383 |
| Hydrophilicity | 0.979 |
| Buriedness | 0.686 |
| Don/acc character | 1.984 |
| SiteScore | 1.154 |
| D Score | 1.033 |
| Kd | — |
| Compound | MTA |
| Residue | . / 101 |
| Chain | Y / 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 | 389.99 Å3 |
| Hydrophobicity | 0.277 |
| Hydrophilicity | 1.029 |
| Buriedness | 0.665 |
| Don/acc character | 1.436 |
| SiteScore | 1.130 |
| D Score | 1.003 |
| Kd | — |