HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

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 6
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

Compound NEG
Residue . / 3216
Chain PL / AA
Non-redundant False
Interacting RNA chains W/AW, A/AA
Volume 671.59 Å3
Hydrophobicity 0.023
Hydrophilicity 1.357
Buriedness 0.761
Don/acc character 2.708
SiteScore 1.042
D Score 0.955

Compound NEG
Residue . / 3218
Chain RL / AA
Non-redundant True
Interacting RNA chains A/AA
Volume 188.65 Å3
Hydrophobicity 0.039
Hydrophilicity 1.104
Buriedness 0.635
Don/acc character 3.695
SiteScore 0.722
D Score 0.659

Compound NEG
Residue . / 3219
Chain SL / AA
Non-redundant True
Interacting RNA chains A/AA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound NEG
Residue . / 3220
Chain TL / AA
Non-redundant False
Interacting RNA chains Z/BA
Volume 466.82 Å3
Hydrophobicity 0.019
Hydrophilicity 1.352
Buriedness 0.703
Don/acc character 1.924
SiteScore 1.003
D Score 0.921

Compound NEG
Residue . / 3221
Chain UL / AA
Non-redundant True
Interacting RNA chains Z/BA
Volume 499.75 Å3
Hydrophobicity 0.030
Hydrophilicity 1.365
Buriedness 0.687
Don/acc character 1.254
SiteScore 0.955
D Score 0.859

Compound NEG
Residue . / 3004
Chain QM / AW
Non-redundant True
Interacting RNA chains Z/BA
Volume 1302.03 Å3
Hydrophobicity 0.095
Hydrophilicity 1.250
Buriedness 0.728
Don/acc character 1.720
SiteScore 1.020
D Score 0.969

Compound NEG
Residue . / 3013
Chain EN / AX
Non-redundant True
Interacting RNA chains Z/BA
Volume 357.41 Å3
Hydrophobicity 0.000
Hydrophilicity 1.281
Buriedness 0.710
Don/acc character 2.284
SiteScore 0.970
D Score 0.900

Compound NEG
Residue . / 3170
Chain PCB / CA
Non-redundant True
Interacting RNA chains AC/CW, EB/CA
Volume 689.09 Å3
Hydrophobicity 0.043
Hydrophilicity 1.349
Buriedness 0.745
Don/acc character 2.333
SiteScore 1.031
D Score 0.947

Compound NEG
Residue . / 3172
Chain RCB / CA
Non-redundant False
Interacting RNA chains EB/CA
Volume 109.76 Å3
Hydrophobicity 0.037
Hydrophilicity 1.174
Buriedness 0.630
Don/acc character 4.777
SiteScore 0.636
D Score 0.527

Compound NEG
Residue . / 3173
Chain SCB / CA
Non-redundant False
Interacting RNA chains EB/CA
Volume -
Hydrophobicity -
Hydrophilicity -
Buriedness -
Don/acc character -
SiteScore -
D Score -

Compound NEG
Residue . / 3174
Chain TCB / CA
Non-redundant True
Interacting RNA chains DC/DA
Volume 493.92 Å3
Hydrophobicity 0.034
Hydrophilicity 1.325
Buriedness 0.689
Don/acc character 1.839
SiteScore 0.994
D Score 0.921

Compound NEG
Residue . / 3175
Chain UCB / CA
Non-redundant True
Interacting RNA chains DC/DA
Volume 437.67 Å3
Hydrophobicity 0.015
Hydrophilicity 1.371
Buriedness 0.687
Don/acc character 0.977
SiteScore 0.923
D Score 0.816

Compound NEG
Residue . / 3002
Chain LDB / CW
Non-redundant False
Interacting RNA chains DC/DA
Volume 1079.42 Å3
Hydrophobicity 0.084
Hydrophilicity 1.271
Buriedness 0.725
Don/acc character 1.555
SiteScore 1.018
D Score 0.961

Compound NEG
Residue . / 3004
Chain QDB / CX
Non-redundant True
Interacting RNA chains DC/DA
Volume 373.18 Å3
Hydrophobicity 0.006
Hydrophilicity 1.331
Buriedness 0.704
Don/acc character 2.040
SiteScore 1.004
D Score 0.929