3DF2

crystal structure of the bacterial ribosome from escherichia coli in complex with hygromycin b. this file contains the 50s subunit of the first 70s ribosome. the entire crystal structure contains two 70s ribosomes.

• Total interactions analyzed: 465
• Total true interactions: 28
• Strongest Interaction:
  • Chains: K-P
  • Int. Res.: 81
  • Norm. En. per Res.: -3.784
• Hub Node: D(4)

All Interactions

Chains	Hydro. Bond Ener. (kJ/mol)	Elec. Ener. (kJ/mol)	VDW. Ener. (kJ/mol)	Tot. Stab. Ener. (kJ/mol)	#int. res.	# Short cont.	#Hydr. int.	#VDW pairs	#salt bridges	#Pot. fav. elec. int	#Pot. unfav. elec. int
V-M	-4.5898	-6.7235	-84.8216	-96.135	51	8	4	3679	0	4	12
D-J	0.0	4.3187	-20.1213	-15.8026	12	2	1	917	0	0	7
D-K	-9.8921	-7.3513	-23.6111	-40.8545	18	2	0	993	0	2	5
D-N	-14.9386	2.2222	-21.0488	-33.7653	17	5	0	1159	0	0	9
D-P	-8.7008	6.2171	-104.185	-106.6687	59	12	1	5447	0	12	12
E-L	-8.3058	0.0	-126.549	-134.8548	47	18	4	6095	1	8	7
E-Q	0.0	0.0	-0.6177	-0.6177	6	0	0	130	0	0	2
E-2	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	0	0
G-4	0.0	0.0	-3.744	-3.744	11	0	0	342	0	2	5
H-Z	0.0	-16.4472	-36.9527	-53.3999	33	5	0	2038	0	7	14
J-Q	0.0	9.1279	-82.6537	-73.5259	46	6	7	4609	0	8	23
J-R	0.0	0.0	-1.7422	-1.7422	8	0	0	355	0	0	4
K-P	-48.3723	-73.5044	-184.63	-306.5067	81	24	3	7706	4	34	33
L-Q	0.0	0.0	-0.0237	-0.0237	7	0	0	20	0	0	2
L-R	0.0	2.6363	-27.9593	-25.323	22	2	0	1249	0	0	12
L-3	-2.5592	40.7317	-196.085	-157.9125	61	8	5	8311	0	4	32
M-W	0.0	0.0	-0.0378	-0.0378	4	0	0	24	0	0	0
M-4	0.0	0.0	-0.0756	-0.0756	4	0	0	37	0	1	1
N-S	0.0	0.0	-15.9827	-15.9827	14	2	0	430	0	2	2
N-0	-4.2052	2.8459	-80.9085	-82.2678	40	7	5	3692	0	11	18
O-W	0.0	-1.601	-0.9936	-2.5946	16	0	0	200	0	6	9
Q-R	-38.1103	0.7276	-268.411	-305.7937	97	46	7	10916	0	22	54
Q-0	0.0	0.0	-14.5487	-14.5487	14	0	0	684	0	0	5
S-0	-18.5174	-16.2051	-79.0077	-113.7302	49	4	8	3504	2	10	7
T-X	-7.2781	11.1965	-80.9394	-77.021	46	15	2	4349	0	10	16
T-2	0.0	0.0	-0.0605	-0.0605	3	0	0	24	0	1	4
W-3	0.0	0.0	-0.0015	-0.0015	2	0	0	4	0	2	2
1-3	0.0	1.146	-19.5789	-18.4329	19	5	0	1155	0	1	7

Interface residues

• V-M: ALA21M, ALA35M, ALA52V, ALA54V, ALA74V, ARG79V, ASP25M, ASP76V, ASP90V, GLN22M, GLN51V, GLN75V, GLN78V, GLN87V, GLN97M, GLY19M, GLY23M, GLY37M, GLY99M, HIS80V, HIS88V, ILE89V, LEU20M, LEU61V, LEU86V, LYS100M, LYS127M, LYS133M, LYS34M, LYS53V, LYS73V, LYS83V, MET136M, PHE130M, PHE56V, PHE91V, PRO81V, PRO84V, PRO98M, SER58V, THR128M, THR129M, THR132M, THR134M, THR24M, TYR57V, TYR82V, VAL131M, VAL135M, VAL36M, VAL77V
• D-J: GLY158D, GLY79J, GLY82J, GLY83J, HIS77J, HIS80J, ILE81J, LYS154D, LYS157D, LYS159D, PHE156D, THR78J
• D-K: ARG128D, ARG13D, ARG31K, ARG70K, ARG71K, ASP18D, ASP73K, GLY19D, GLY74K, HIS29K, ILE22D, PHE15D, PRO23D, PRO72K, SER21D, SER75K, THR16D, VAL20D
• D-N: ALA119D, ALA196D, ARG2N, ARG4N, ASN167D, GLN164D, GLY115D, GLY117D, GLY166D, HIS3N, LYS114D, LYS116D, LYS123D, MET165D, MET1N, PHE118D, THR197D
• D-P: ALA57P, ARG13D, ARG179D, ARG184D, ARG52P, ASN185D, ASN2P, ASP181D, ASP18D, GLN11P, GLN6P, GLN74P, GLN9P, GLU10P, GLU17D, GLU28D, GLU8P, GLY10D, GLY19D, GLY53P, HIS55P, HIS76P, ILE14D, ILE22D, ILE27D, ILE3P, ILE4P, LEU186D, LEU187D, LEU188D, LEU54P, LEU7P, LYS13P, LYS5P, LYS7D, LYS8D, MET11D, MET12P, PHE15D, PHE73P, PRO23D, PRO78P, SER1P, SER21D, SER56P, SER77P, THR12D, THR16D, THR197D, THR25D, THR75P, TRP30P, VAL20D, VAL24D, VAL26D, VAL32P, VAL79P, VAL80P, VAL9D
• E-L: ALA104E, ALA182E, ALA26E, ALA36E, ALA9L, ARG114E, ARG117E, ARG21L, ARG2L, ASN24E, ASN4L, ASP184E, GLN115E, GLN30E, GLN94E, GLU10L, GLU111E, GLU25E, HIS29E, ILE108E, ILE181E, LEU105E, LEU109E, LEU112E, LEU180E, LEU27E, LEU3L, LEU6L, LYS13L, PHE183E, PHE23E, PHE85E, PRO177E, PRO8L, SER107E, SER110E, SER12L, SER179E, SER42L, SER7L, THR5L, VAL113E, VAL178E, VAL28E, VAL31E, VAL32E, VAL33E
• E-Q: ALA1Q, ARG2Q, ARG40E, ARG44E, GLN46E, VAL83E
• E-2: LYS372, THR53E
• G-4: ALA294, ARG169G, ASN134, CYS274, GLU304, LYS171G, LYS324, PRO155G, PRO314, SER284, VAL167G
• H-Z: ALA23H, ALA26H, ALA36H, ARG27H, ARG37Z, ARG57Z, ASN28H, ASP60Z, ASP65Z, GLN33H, GLU41Z, GLY24H, GLY34H, GLY63Z, HIS36Z, ILE59Z, ILE64Z, LYS42H, LYS61Z, LYS62Z, MET1H, MET56Z, PHE38Z, PHE46Z, PRO32H, PRO38H, THR40H, THR66Z, TRP39Z, VAL31H, VAL3H, VAL40Z, VAL58Z
• J-Q: ALA42J, ALA62Q, ALA66Q, ALA67Q, ALA68Q, ALA6J, ALA98Q, ARG34J, ARG35J, ARG37J, ARG63Q, ARG69Q, ASN65Q, ASN71Q, ASP96Q, GLN55Q, GLN58Q, GLN70Q, GLU31J, GLU43J, GLY38J, HIS40J, HIS47J, ILE61Q, ILE64Q, ILE93Q, LEU59Q, LEU94Q, LYS102Q, LYS12J, LYS2J, LYS39J, LYS41J, LYS7J, LYS92Q, MET1J, PHE100Q, PHE4J, PHE56Q, PRO46J, THR3J, THR45J, THR5J, TRP60Q, TYR44J, VAL99Q
• J-R: ARG13R, ARG21R, GLN18R, HIS12R, MET1J, THR19R, VAL14R, VAL20R
• K-P: ALA119K, ALA11K, ALA41P, ALA48P, ALA57P, ALA83K, ARG100P, ARG102P, ARG105K, ARG108K, ARG38P, ARG61P, ARG64K, ARG70K, ARG71K, ARG71P, ARG78K, ASN65P, ASN82K, ASN9K, ASP73K, ASP80K, GLN40P, GLN74P, GLU101P, GLU110K, GLU121K, GLU33P, GLU43P, GLU67P, GLU70P, GLY101K, GLY34P, GLY66P, GLY68K, GLY68P, GLY74K, GLY81K, HIS76P, ILE47P, ILE63P, ILE77K, ILE99K, LEU118K, LYS36P, LYS62P, LYS66K, LYS67K, MET113K, PHE100K, PHE42P, PHE58P, PHE73P, PHE79K, PRO102K, PRO120K, PRO72K, PRO78P, SER35P, SER56P, SER64P, SER75K, SER77P, THR104K, THR59P, THR75P, TRP30P, TYR97P, VAL103K, VAL10K, VAL122K, VAL29P, VAL31P, VAL32P, VAL60P, VAL69K, VAL69P, VAL72P, VAL76K, VAL79P, VAL80P
• L-Q: ARG12Q, ARG21L, ARG5Q, GLY22L, GLY24L, ILE23L, PHE35Q
• L-R: ARG21L, ARG80R, ARG84R, GLN86R, GLY20L, GLY22L, GLY24L, GLY26L, GLY28L, GLY31L, GLY32L, HIS35L, HIS82R, ILE23L, LEU27L, LYS29L, LYS81R, LYS85R, PHE77R, SER25L, THR30L, TYR83R
• L-3: ALA103, ALA263, ALA473, ALA593, ALA93, ARG123, ARG293, ARG47L, ARG48L, ARG59L, ARG60L, ARG73, ASN273, ASP533, CYS603, GLU51L, GLY49L, GLY523, GLY52L, GLY553, GLY65L, GLY83, HIS233, HIS253, HIS303, ILE33, ILE583, LEU283, LEU433, LEU543, LEU563, LEU57L, LEU613, LEU61L, LYS113, LYS143, LYS153, LYS223, LYS23, LYS243, LYS43, LYS463, LYS513, LYS63L, MET483, MET55L, PHE133, PHE213, PHE50L, PHE64L, PHE66L, PRO56L, PRO623, PRO62L, SER503, THR53, TYR58L, TYR633, VAL493, VAL573, VAL63
• M-W: GLY85M, LYS11M, LYS86M, SER8W
• M-4: LEU119M, LYS118M, LYS84, LYS94
• N-S: ALA108N, ARG103N, ASN107N, ASN40S, ASP106N, CYS100N, GLY101N, LYS41S, LYS42S, PHE102N, PRO109N, THR37S, THR39S, TYR38S
• N-0: ALA111N, ALA550, ARG118N, ARG390, ARG490, ARG510, ARG90N, ARG96N, ASP117N, CYS100N, GLU114N, GLU120N, GLY101N, GLY460, HIS370, HIS400, HIS410, ILE113N, ILE33N, ILE34N, ILE420, ILE540, ILE97N, LEU380, LEU38N, LEU98N, LYS35N, LYS520, LYS560, LYS99N, MET110N, PHE102N, PRO109N, SER119N, THR430, TYR112N, TYR470, TYR480, VAL116N, VAL530
• O-W: ALA46W, ALA48W, ARG13O, ARG16O, ARG40W, ASN49W, GLN19O, GLU20O, GLY47W, HIS45W, LYS17O, LYS61W, PHE44W, PHE78W, PRO73W, VAL50W
• Q-R: ALA104Q, ALA107Q, ALA112Q, ALA114Q, ALA115Q, ALA3R, ALA41Q, ALA42R, ALA45Q, ALA85Q, ALA95Q, ALA98Q, ARG12Q, ARG13R, ARG47Q, ARG49Q, ARG50Q, ARG52Q, ARG78R, ARG79R, ARG84R, ARG91Q, ASN43R, ASP101Q, ASP90Q, ASP96Q, GLN11R, GLN19Q, GLN36Q, GLN43Q, GLN6R, GLN86R, GLN87R, GLU110Q, GLU45R, GLU46R, GLU88Q, GLY42Q, GLY44R, GLY50R, GLY88R, GLY9R, HIS12R, HIS89R, ILE16Q, ILE39Q, ILE41R, ILE49R, ILE74R, ILE89Q, ILE93Q, ILE97Q, LEU108Q, LEU39R, LEU82Q, LEU94Q, LYS102Q, LYS10R, LYS111Q, LYS113Q, LYS15Q, LYS40Q, LYS48R, LYS73R, LYS76R, LYS83Q, LYS85R, LYS92Q, MET1R, MET40R, PHE100Q, PHE105Q, PHE35Q, PHE53R, PHE5R, PHE77R, PHE78Q, PRO52R, SER7R, SER86Q, THR106Q, TYR2R, TYR31Q, TYR44Q, TYR46Q, TYR83R, VAL103Q, VAL109Q, VAL14R, VAL38Q, VAL47R, VAL4R, VAL51R, VAL72R, VAL75R, VAL87Q, VAL99Q
• Q-0: ALA26Q, ARG120, ARG29Q, ARG90, GLY25Q, LYS110, LYS60, MET140, PRO70, SER100, SER28Q, THR80, TYR24Q, VAL30Q
• S-0: ALA200, ALA21S, ALA230, ALA32S, ALA43S, ALA440, ALA44S, ARG120, ARG150, ARG160, ARG18S, ARG390, ARG99S, ASN40S, ASP190, ASP22S, ASP34S, GLN15S, GLN31S, GLU350, GLU78S, HIS180, HIS370, HIS410, ILE35S, ILE420, LEU19S, LEU210, LEU23S, LEU270, LEU33S, LEU36S, LEU380, LYS16S, LYS27S, LYS360, LYS41S, SER260, SER280, SER30S, THR220, THR250, THR37S, THR39S, THR430, TYR38S, VAL17S, VAL20S, VAL240
• T-X: ALA13T, ALA32X, ALA33X, ALA35T, ALA46T, ARG12T, ARG23X, ARG29X, ARG6T, ASN27X, GLN25X, GLN31X, GLU17X, GLU4T, GLU52T, GLU5T, GLY35X, HIS15T, ILE30T, LEU11T, LEU14X, LEU18X, LEU19X, LEU21X, LEU22X, LEU28X, LEU32T, LEU43X, LEU50T, LEU57X, LEU7T, LEU8T, LYS33T, LYS49T, LYS54X, LYS9T, MET30X, PHE26X, PHE51T, PRO14T, SER34X, VAL10T, VAL16T, VAL34T, VAL47T, VAL50X
• T-2: ARG412, ARG73T, ILE74T
• W-3: ARG54W, LYS383
• 1-3: ARG51, GLU61, HIS303, ILE313, ILE81, LEU323, LYS343, LYS353, LYS371, LYS403, LYS71, LYS91, PHE191, THR211, THR221, THR231, THR333, THR373, TYR201