1VS6

crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in remark 400.

• Total interactions analyzed: 465
• Total true interactions: 29
• Strongest Interaction:
  • Chains: N-0
  • Int. Res.: 50
  • Norm. En. per Res.: -2.6297
• 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	-33.348	1.0202	-100.466	-132.7938	54	27	2	4796	0	6	15
C-2	0.0	0.0	-0.0012	-0.0012	2	0	0	4	0	0	0
D-J	0.0	3.4104	-39.3246	-35.9143	15	2	1	1388	0	0	7
D-K	0.0	8.4691	-23.3994	-14.9303	17	1	0	925	0	7	2
D-N	-11.1787	8.9579	-19.7801	-22.0009	15	4	0	805	0	1	10
D-P	-3.9526	0.1629	-119.804	-123.5937	60	23	1	5678	0	12	14
E-L	-12.2868	-2.1488	-62.1333	-76.5689	41	5	1	2871	2	16	10
E-Q	0.0	0.0	-0.3081	-0.3081	5	0	0	57	0	0	3
E-S	0.0	0.0	-0.2322	-0.2322	4	0	0	46	0	0	1
G-4	0.0	0.0	-0.1705	-0.1705	9	0	0	54	0	3	2
H-Z	0.0	12.9272	-15.1266	-2.1994	39	0	0	1460	0	5	13
J-Q	-4.3821	17.3759	-96.5575	-83.5637	52	21	5	5642	0	10	28
J-R	0.0	0.0	-7.0602	-7.0602	15	5	0	969	0	1	5
K-P	-14.6984	44.0626	-167.982	-138.6179	71	24	1	6467	0	31	37
L-Q	0.0	0.0	-0.0137	-0.0137	3	0	0	10	0	0	2
L-R	-14.2063	1.3543	-5.2308	-18.0827	10	2	0	294	0	0	14
L-3	-14.7888	37.4142	-166.377	-143.7516	58	65	1	7341	0	2	30
M-W	0.0	0.0	-0.1547	-0.1547	4	0	0	41	0	0	1
M-I	0.0	0.0	-0.0433	-0.0433	2	0	0	21	0	0	1
N-S	-3.9073	0.0	-21.3876	-25.2949	15	3	0	624	0	2	2
N-0	-26.6711	-10.6365	-94.1757	-131.4833	50	23	0	4679	2	23	28
O-W	0.0	4.8677	-43.5209	-38.6532	27	16	1	2778	0	6	17
Q-R	-4.3888	42.0242	-203.427	-165.7916	93	43	5	9898	1	22	51
Q-0	0.0	8.4269	-8.6374	-0.2104	13	0	0	599	0	0	5
S-0	-2.2648	7.0508	-82.5162	-77.7302	44	5	7	3571	1	9	6
T-X	0.0	38.8285	-101.716	-62.8875	49	24	2	5189	0	5	11
T-2	0.0	0.0	-0.0278	-0.0278	5	0	0	19	0	0	7
W-3	0.0	0.0	-0.0793	-0.0793	2	0	0	21	0	0	1
1-3	0.0	5.2443	-1.0805	4.1638	20	5	0	1295	0	3	9

Interface residues

• V-M: ALA35M, ALA52V, ALA54V, ALA74V, ARG38M, ARG79V, ASP25M, ASP76V, ASP90V, GLN22M, GLN51V, GLN75V, GLN78V, GLN97M, GLY23M, GLY37M, GLY99M, HIS80V, HIS88V, ILE126M, ILE29V, ILE89V, ILE96M, LEU124M, LEU86V, LYS123M, LYS127M, LYS133M, LYS34M, LYS53V, LYS83V, LYS85V, MET136M, PHE130M, PHE56V, PHE91V, PRO125M, PRO81V, PRO84V, PRO98M, SER58V, THR129M, THR132M, THR134M, THR24M, TYR31V, TYR57V, TYR82V, VAL131M, VAL135M, VAL26M, VAL36M, VAL77V, VAL92V
• C-2: ARG142, ARG47C
• D-J: GLY153D, GLY158D, GLY79J, GLY82J, GLY83J, HIS77J, HIS80J, ILE81J, ILE84J, LYS154D, LYS157D, LYS159D, PHE156D, THR78J, VAL155D
• D-K: ARG31K, ARG70K, ARG71K, ASP18D, ASP73K, GLU17D, GLY19D, GLY74K, ILE14D, ILE22D, PHE127D, PHE15D, PRO72K, SER75K, THR12D, THR16D, VAL20D
• D-N: ALA196D, ARG2N, ARG4N, ASN167D, GLY115D, GLY117D, GLY166D, HIS3N, LYS114D, LYS116D, LYS123D, MET165D, MET1N, SER113D, THR197D
• D-P: ALA41P, ALA57P, ARG13D, ARG179D, ARG184D, ASN185D, ASN2P, ASP181D, ASP18D, ASP81P, GLN11P, GLN40P, GLN6P, GLN9P, GLU10P, GLU17D, GLU28D, GLU33P, GLU8P, GLY10D, GLY19D, GLY34P, GLY6D, HIS55P, HIS76P, ILE14D, ILE27D, ILE3P, ILE4P, LEU186D, LEU187D, LEU188D, LEU7P, LYS13P, LYS5P, LYS7D, LYS8D, MET11D, MET12P, PHE15D, PRO23D, PRO78P, SER1P, SER21D, SER35P, SER56P, SER77P, THR12D, THR16D, THR197D, THR25D, THR59P, VAL24D, VAL26D, VAL31P, VAL32P, VAL5D, VAL79P, VAL80P, VAL9D
• E-L: ALA15L, ALA182E, ALA26E, ALA9L, ARG114E, ARG18L, ASN24E, ASP184E, GLN115E, GLN30E, GLU10L, GLU111E, GLU25E, GLY11L, GLY16L, GLY20L, GLY28L, HIS29E, ILE108E, ILE181E, LEU112E, LEU180E, LEU19L, LEU27E, LYS13L, LYS14L, LYS17L, LYS185E, LYS29L, MET100E, PHE183E, PHE23E, PHE85E, PRO177E, SER12L, SER179E, VAL178E, VAL28E, VAL31E, VAL32E, VAL33E
• E-Q: ALA1Q, ALA45E, ALA87E, ARG2Q, LYS47E
• E-S: ARG67E, ARG92S, GLY66E, THR65E
• G-4: ALA294, ARG169G, GLU172G, GLU304, PRO155G, PRO314, SER284, VAL167G, VAL168G
• H-Z: ALA23H, ALA26H, ALA36H, ALA52Z, ARG27H, ARG49Z, ARG56Z, ARG59Z, ASN28H, ASN33Z, ASN43H, ASP35Z, ASP58Z, CYS37Z, GLN33H, GLY24H, GLY34H, GLY55Z, HIS41Z, LEU32Z, LEU34Z, LYS41H, LYS42H, LYS47Z, LYS62Z, MET1H, PHE29H, PHE60Z, PRO32H, PRO38H, PRO42Z, SER38Z, THR40H, THR53Z, TYR25H, VAL31H, VAL36Z, VAL37H, VAL57Z
• J-Q: ALA42J, ALA62Q, ALA66Q, ALA67Q, ALA68Q, ALA6J, ALA95Q, ALA98Q, ARG34J, ARG35J, ARG37J, ARG49Q, ARG52Q, ARG54Q, ARG63Q, ARG69Q, ASN65Q, ASN71Q, ASP96Q, GLN55Q, GLN58Q, GLN70Q, GLU31J, GLU43J, GLY38J, HIS40J, HIS47J, ILE64Q, ILE93Q, ILE97Q, LEU59Q, LEU94Q, LYS102Q, LYS2J, LYS39J, LYS41J, LYS92Q, MET1J, PHE100Q, PHE105Q, PHE4J, PHE56Q, PRO46J, PRO8J, SER74Q, THR3J, THR45J, THR5J, TRP60Q, TYR44J, VAL48J, VAL99Q
• J-R: ARG13R, GLN11R, GLN18R, GLU16R, GLY17R, LYS2J, LYS73R, LYS97R, MET1J, PHE4J, SER15R, THR19R, THR3J, VAL14R, VAL20R
• K-P: ALA11K, ALA57P, ALA83K, ARG102P, ARG105K, ARG108K, ARG50P, ARG61P, ARG64K, ARG70K, ARG71K, ARG71P, ARG78K, ASN65P, ASN82K, ASN9K, ASP73K, ASP80K, ASP81P, GLN74P, GLU110K, GLU121K, GLU33P, GLU67P, GLU70P, GLY101K, GLY104P, GLY34P, GLY44P, GLY66P, GLY68K, GLY68P, GLY74K, GLY81K, HIS76P, ILE116K, ILE63P, ILE77K, LYS28P, LYS36P, LYS37P, LYS62P, LYS66K, LYS67K, MET113K, PHE100K, PHE73P, PHE79K, PRO102K, PRO120K, PRO72K, PRO78P, SER109K, SER35P, SER64P, SER75K, SER77P, THR103P, THR59P, THR75P, VAL103K, VAL122K, VAL31P, VAL45P, VAL60P, VAL69K, VAL69P, VAL72P, VAL76K, VAL79P, VAL80P
• L-Q: ARG12Q, ARG33L, GLY32L
• L-R: ARG33L, ARG80R, ARG84R, GLY32L, GLY34L, HIS35L, HIS82R, LYS81R, LYS85R, TYR83R
• L-3: ALA103, ALA263, ALA643, ALA72L, ALA93, ARG123, ARG293, ARG413, ARG443, ARG59L, ARG60L, ARG69L, ARG73, ASN273, ASP533, GLN54L, GLU51L, GLY523, GLY53L, GLY553, GLY65L, GLY83, HIS233, HIS253, HIS303, HIS423, ILE313, ILE583, ILE73L, LEU283, LEU433, LEU543, LEU563, LEU57L, LEU61L, LYS113, LYS223, LYS243, LYS513, LYS63L, MET483, MET55L, PHE133, PHE64L, PHE66L, PRO453, PRO56L, PRO623, PRO62L, SER503, SER68L, THR53, THR67L, TYR58L, TYR633, VAL493, VAL573, VAL63
• M-W: GLY7W, LYS84M, SER8W, THR9W
• M-I: LYS58M, LYS94I
• N-S: ALA104N, ALA108N, ARG103N, ASN107N, ASN40S, ASP106N, GLY101N, GLY105N, LEU36S, LYS41S, LYS42S, PHE102N, THR37S, THR39S, TYR38S
• N-0: ALA111N, ALA122N, ALA124N, ALA125N, ALA126N, ALA550, ARG118N, ARG390, ARG490, ARG510, ARG96N, ASP117N, ASP450, CYS100N, GLU114N, GLU120N, GLU123N, GLU127N, GLU32N, GLY101N, GLY460, GLY500, HIS370, HIS400, HIS410, ILE113N, ILE33N, ILE420, ILE540, ILE97N, LEU115N, LEU380, LEU38N, LEU98N, LYS121N, LYS310, LYS360, LYS520, LYS560, LYS99N, PHE102N, SER119N, SER260, THR430, TYR112N, TYR470, TYR480, VAL116N, VAL240, VAL530
• O-W: ARG15O, ARG16O, ARG76W, ARG7O, ASN43O, ASN75W, ASP63W, GLN19O, GLU20O, GLU84W, GLY22O, GLY41W, GLY44O, ILE79W, LEU18O, LEU21O, LYS17O, LYS43W, LYS65W, LYS74W, LYS77W, PHE44W, PHE78W, PRO42O, PRO73W, THR42W, VAL50W
• Q-R: ALA104Q, ALA107Q, ALA112Q, ALA34Q, ALA3R, ALA41Q, ALA42R, ALA45Q, ALA85Q, ALA95Q, ARG12Q, ARG13R, ARG47Q, ARG49Q, ARG50Q, ARG78R, ARG79R, ARG80R, ARG84R, ARG91Q, ASP101Q, ASP48Q, ASP55R, ASP90Q, ASP96Q, GLN11R, GLN19Q, GLN36Q, GLN43Q, GLN51Q, GLN6R, GLN86R, GLN87R, GLU110Q, GLU45R, GLU46R, GLU88Q, GLY42Q, GLY44R, GLY50R, GLY56R, GLY9R, HIS12R, HIS89R, ILE16Q, ILE39Q, ILE41R, ILE89Q, ILE93Q, ILE97Q, LEU108Q, LEU39R, LEU82Q, LEU94Q, LYS102Q, LYS10R, LYS111Q, LYS15Q, LYS40Q, LYS53Q, LYS73R, LYS76R, LYS81R, LYS85R, LYS92Q, MET40R, PHE100Q, PHE105Q, PHE35Q, PHE53R, PHE5R, PHE77R, PHE93R, PRO52R, SER86Q, THR106Q, TRP60Q, TYR2R, TYR31Q, TYR44Q, TYR46Q, VAL103Q, VAL109Q, VAL14R, VAL38Q, VAL38R, VAL47R, VAL4R, VAL51R, VAL54R, VAL75R, VAL87Q, VAL99Q
• Q-0: ALA26Q, ARG27Q, ARG29Q, ARG90, GLY22Q, GLY25Q, LYS110, PRO70, SER100, SER28Q, THR80, TYR24Q, VAL30Q
• S-0: ALA200, ALA21S, ALA230, ALA43S, ALA44S, ARG120, ARG150, ARG160, ARG18S, ASN40S, ASP190, ASP22S, ASP34S, GLN15S, GLN31S, GLU350, GLY340, HIS180, HIS370, ILE24S, ILE35S, ILE420, LEU19S, LEU210, LEU23S, LEU270, LEU33S, LEU36S, LEU380, LYS16S, LYS360, LYS41S, SER260, SER280, THR220, THR250, THR320, THR37S, THR39S, THR430, TYR38S, VAL17S, VAL20S, VAL240
• T-X: ALA13T, ALA32X, ALA33X, ALA35T, ALA46T, ALA99T, ARG12T, ARG23X, ARG29X, ARG3T, ARG47X, ARG6T, ASN20X, ASN27X, GLN25X, GLN31X, GLN48T, GLU17X, GLU24X, GLU52T, GLY97T, GLY98T, HIS15T, LEU11T, LEU18X, LEU19X, LEU21X, LEU22X, LEU28X, LEU32T, LEU43X, LEU50T, LEU7T, LEU8T, LYS33T, LYS49T, LYS9T, MET30X, PHE26X, PHE51T, PHE95T, PRO14T, THR16X, VAL10T, VAL16T, VAL34T, VAL47T, VAL50X, VAL96T
• T-2: ARG412, ARG77T, HIS70T, ILE74T, LYS462
• W-3: ARG38W, ARG393
• 1-3: ALA363, ASN251, ILE313, ILE81, LEU101, LEU323, LYS21, LYS241, LYS343, LYS353, LYS403, LYS71, LYS91, PHE381, THR211, THR221, THR231, THR333, THR373, VAL111