Complex 4w2i
System information
| Experimental technique | X-ray |
| Experimental resolution | 2.70 |
| System mass | 4555.29 kDa |
| Deposition year | 2014 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 4w2i |
| Reference | Polikanov Yury S., Szal Teresa, Jiang Fuyan, Gupta Pulkit, Matsuda Ryoichi, Shiozuka Masataka, Steitz Thomas A., Vázquez-Laslop Nora, Mankin Alexander S.. . Negamycin Interferes with Decoding and Translocation by Simultaneous Interaction with rRNA and tRNA Molecular Cell |
| Equivalence Class |
NR_all_65795.87,
NR_all_97519.80,
NR_all_19951.100
BGSU version: 4.48 |
| Compound | NEG |
| Residue | . / 3004 |
| Chain | QDB / CX |
| Non-redundant | True |
| Interacting RNA chains | DC/DA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | DC/DA: rRNA |
| RNA family global | rRNA |
| Volume | 375.93 Å3 |
| Hydrophobicity | 0.028 |
| Hydrophilicity | 1.219 |
| Buriedness | 0.704 |
| Don/acc character | 2.280 |
| SiteScore | 1.154 |
| D Score | 0.965 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3216 |
| Chain | PL / AA |
| Non-redundant | True |
| Interacting RNA chains | A/AA, W/AW |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/AA: rRNA, W/AW: tRNA |
| RNA family global | multiple |
| Volume | 179.05 Å3 |
| Hydrophobicity | 0.017 |
| Hydrophilicity | 1.766 |
| Buriedness | 0.595 |
| Don/acc character | 0.618 |
| SiteScore | 1.000 |
| D Score | 0.617 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3217 |
| Chain | QL / AA |
| Non-redundant | True |
| Interacting RNA chains | A/AA |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/AA: rRNA |
| RNA family global | rRNA |
| Volume | 583.44 Å3 |
| Hydrophobicity | 0.132 |
| Hydrophilicity | 1.247 |
| Buriedness | 0.769 |
| Don/acc character | 1.969 |
| SiteScore | 1.198 |
| D Score | 0.995 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3218 |
| Chain | RL / AA |
| Non-redundant | True |
| Interacting RNA chains | A/AA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/AA: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | NEG |
| Residue | . / 3219 |
| Chain | SL / AA |
| Non-redundant | True |
| Interacting RNA chains | A/AA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/AA: rRNA |
| RNA family global | rRNA |
| Volume | 351.92 Å3 |
| Hydrophobicity | 0.011 |
| Hydrophilicity | 1.225 |
| Buriedness | 0.562 |
| Don/acc character | 1.234 |
| SiteScore | 1.059 |
| D Score | 0.878 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3220 |
| Chain | TL / AA |
| Non-redundant | True |
| Interacting RNA chains | Z/BA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | Z/BA: rRNA |
| RNA family global | rRNA |
| Volume | 535.08 Å3 |
| Hydrophobicity | 0.045 |
| Hydrophilicity | 0.998 |
| Buriedness | 0.545 |
| Don/acc character | 3.273 |
| SiteScore | 1.056 |
| D Score | 0.942 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3221 |
| Chain | UL / AA |
| Non-redundant | True |
| Interacting RNA chains | Z/BA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | Z/BA: rRNA |
| RNA family global | rRNA |
| Volume | 354.66 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.321 |
| Buriedness | 0.701 |
| Don/acc character | 1.366 |
| SiteScore | 1.028 |
| D Score | 0.771 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3222 |
| Chain | VL / AA |
| Non-redundant | True |
| Interacting RNA chains | Z/BA |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | Z/BA: rRNA |
| RNA family global | rRNA |
| Volume | 298.41 Å3 |
| Hydrophobicity | 0.017 |
| Hydrophilicity | 1.784 |
| Buriedness | 0.632 |
| Don/acc character | 1.204 |
| SiteScore | 1.036 |
| D Score | 0.649 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3004 |
| Chain | QM / AW |
| Non-redundant | True |
| Interacting RNA chains | Z/BA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | Z/BA: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | NEG |
| Residue | . / 3013 |
| Chain | EN / AX |
| Non-redundant | True |
| Interacting RNA chains | Z/BA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | Z/BA: rRNA |
| RNA family global | rRNA |
| Volume | 354.32 Å3 |
| Hydrophobicity | 0.017 |
| Hydrophilicity | 1.236 |
| Buriedness | 0.712 |
| Don/acc character | 1.949 |
| SiteScore | 1.114 |
| D Score | 0.906 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3170 |
| Chain | PCB / CA |
| Non-redundant | True |
| Interacting RNA chains | EB/CA, AC/CW |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | AC/CW: tRNA, EB/CA: rRNA |
| RNA family global | multiple |
| Volume | 141.66 Å3 |
| Hydrophobicity | 0.043 |
| Hydrophilicity | 1.364 |
| Buriedness | 0.559 |
| Don/acc character | 1.081 |
| SiteScore | 0.954 |
| D Score | 0.699 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3171 |
| Chain | QCB / CA |
| Non-redundant | True |
| Interacting RNA chains | EB/CA |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | EB/CA: rRNA |
| RNA family global | rRNA |
| Volume | 397.19 Å3 |
| Hydrophobicity | 0.061 |
| Hydrophilicity | 1.325 |
| Buriedness | 0.785 |
| Don/acc character | 2.282 |
| SiteScore | 1.151 |
| D Score | 0.906 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3172 |
| Chain | RCB / CA |
| Non-redundant | True |
| Interacting RNA chains | EB/CA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | EB/CA: rRNA |
| RNA family global | rRNA |
| Volume | 48.02 Å3 |
| Hydrophobicity | 0.055 |
| Hydrophilicity | 1.013 |
| Buriedness | 0.525 |
| Don/acc character | 4.565 |
| SiteScore | 0.681 |
| D Score | 0.464 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3173 |
| Chain | SCB / CA |
| Non-redundant | True |
| Interacting RNA chains | EB/CA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | EB/CA: rRNA |
| RNA family global | rRNA |
| Volume | 81.29 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.464 |
| Buriedness | 0.681 |
| Don/acc character | 0.944 |
| SiteScore | 0.734 |
| D Score | 0.352 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3174 |
| Chain | TCB / CA |
| Non-redundant | True |
| Interacting RNA chains | DC/DA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | DC/DA: rRNA |
| RNA family global | rRNA |
| Volume | 445.56 Å3 |
| Hydrophobicity | 0.027 |
| Hydrophilicity | 1.978 |
| Buriedness | 0.694 |
| Don/acc character | 0.978 |
| SiteScore | 1.147 |
| D Score | 0.711 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3175 |
| Chain | UCB / CA |
| Non-redundant | True |
| Interacting RNA chains | DC/DA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | DC/DA: rRNA |
| RNA family global | rRNA |
| Volume | 460.65 Å3 |
| Hydrophobicity | 0.043 |
| Hydrophilicity | 1.632 |
| Buriedness | 0.686 |
| Don/acc character | 0.726 |
| SiteScore | 1.142 |
| D Score | 0.820 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3176 |
| Chain | VCB / CA |
| Non-redundant | True |
| Interacting RNA chains | DC/DA |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | DC/DA: rRNA |
| RNA family global | rRNA |
| Volume | 295.32 Å3 |
| Hydrophobicity | 0.043 |
| Hydrophilicity | 1.729 |
| Buriedness | 0.635 |
| Don/acc character | 1.265 |
| SiteScore | 1.059 |
| D Score | 0.694 |
| Kd | — |
| Compound | NEG |
| Residue | . / 3177 |
| Chain | WCB / CA |
| Non-redundant | True |
| Interacting RNA chains | DC/DA |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | DC/DA: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | NEG |
| Residue | . / 3002 |
| Chain | LDB / CW |
| Non-redundant | True |
| Interacting RNA chains | DC/DA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | DC/DA: rRNA |
| RNA family global | rRNA |
| Volume | 91.58 Å3 |
| Hydrophobicity | 0.068 |
| Hydrophilicity | 1.195 |
| Buriedness | 0.521 |
| Don/acc character | 0.973 |
| SiteScore | 0.817 |
| D Score | 0.587 |
| Kd | — |