3OFZ

crystal structure of the e. coli ribosome bound to clindamycin. this file contains the 50s subunit of the first 70s ribosome bound to clindamycin.

• Total interactions analyzed: 465
• Total true interactions: 29
• Strongest Interaction:
  • Chains: K-P
  • Int. Res.: 75
  • Norm. En. per Res.: -3.9464
• 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
D-J	0.0	2.7891	-21.1258	-18.3366	11	1	1	860	0	0	7
D-K	0.0	-6.8331	-28.6811	-35.5142	19	1	0	1019	0	2	5
D-N	-5.1231	3.9441	-21.7943	-22.9733	16	2	0	1139	0	0	11
D-P	-5.377	9.8104	-140.652	-136.2186	60	14	5	6815	2	12	11
E-L	-9.2078	2.7744	-105.231	-111.6645	49	4	6	5726	1	8	6
E-Q	0.0	0.0	-0.409	-0.409	5	0	0	103	0	0	2
E-2	0.0	0.0	-0.0119	-0.0119	2	0	0	11	0	0	0
G-4	-6.8784	-19.4902	-9.13	-35.4986	10	0	0	381	1	2	4
H-X	-16.1766	-14.4355	-39.1578	-69.77	36	8	0	2151	0	7	12
J-Q	0.0	0.0	-49.1457	-49.1457	51	21	5	4800	0	8	23
J-R	0.0	0.0	-6.9345	-6.9345	14	0	0	556	0	0	4
K-P	-71.7682	-57.3811	-166.828	-295.9773	75	19	3	6965	3	28	30
L-Q	0.0	0.0	-0.0032	-0.0032	9	0	0	8	0	0	2
L-R	-14.6471	2.6582	-33.0399	-45.0288	23	4	1	1433	0	0	12
L-3	-16.0789	15.2995	-191.958	-192.7374	56	21	5	8394	0	4	35
M-V	-15.3855	-4.5265	-86.6059	-106.5179	51	7	4	3904	0	5	11
M-W	0.0	0.0	-0.0108	-0.0108	6	0	0	14	0	0	0
M-4	0.0	0.0	-0.0052	-0.0052	3	0	0	9	0	0	1
N-P	0.0	0.0	-0.0021	-0.0021	2	0	0	3	0	0	0
N-S	0.0	0.0	-8.6251	-8.6251	11	0	0	315	0	2	2
N-0	-14.1399	5.5321	-77.4437	-86.0515	38	3	5	3677	0	9	20
O-W	0.0	-9.0171	-6.7565	-15.7735	20	0	0	445	0	5	10
Q-R	-36.383	-15.1984	-221.104	-272.6854	100	49	8	11450	3	23	51
Q-0	0.0	16.2037	-13.0308	3.1729	13	1	0	664	0	0	6
S-0	-10.333	-16.6606	-73.5896	-100.5832	48	6	8	4034	2	11	10
T-Y	0.0	4.5209	-69.0339	-64.513	45	6	2	3840	0	7	14
T-2	0.0	0.0	-0.4533	-0.4533	8	0	0	100	0	1	4
W-3	0.0	0.0	-0.0044	-0.0044	3	0	0	8	0	2	2
1-3	0.0	1.2598	-21.1518	-19.892	17	3	0	1022	0	1	6

Interface residues

• D-J: GLY158D, GLY79J, GLY82J, HIS77J, HIS80J, ILE81J, LYS154D, LYS157D, LYS159D, PHE156D, THR78J
• D-K: ARG128D, ARG13D, ARG31K, ARG70K, ARG71K, ASP18D, ASP73K, GLY19D, GLY74K, HIS29K, ILE14D, ILE22D, PHE15D, PRO23D, PRO72K, SER21D, SER75K, THR16D, VAL20D
• D-N: ALA119D, ALA196D, ARG2N, ARG4N, ASN167D, 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, VAL29D, VAL32P, VAL79P, VAL80P, VAL9D
• E-L: ALA104E, ALA182E, ALA26E, ALA34E, 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, TYR35E, VAL113E, VAL178E, VAL28E, VAL31E, VAL32E, VAL33E
• E-Q: ALA1Q, ARG2Q, ARG44E, GLN46E, VAL83E
• E-2: LYS372, THR53E
• G-4: ALA294, ARG169G, CYS274, GLU304, LYS171G, LYS324, PRO155G, PRO314, SER284, VAL167G
• H-X: ALA23H, ALA26H, ALA39H, ARG27H, ARG36X, ARG44X, ARG56X, ASN28H, ASP59X, GLN33H, GLU40X, GLY24H, GLY34H, GLY62X, HIS35X, ILE58X, ILE63X, LEU6H, LYS41H, LYS43X, LYS60X, LYS61X, MET1H, MET55X, PHE29H, PHE37X, PHE45X, PRO32H, PRO38H, SER41X, THR40H, TRP38X, VAL31H, VAL39X, VAL3H, VAL57X
• J-Q: ALA42J, ALA62Q, ALA66Q, ALA67Q, ALA68Q, ALA6J, ALA95Q, ALA98Q, ARG34J, ARG35J, ARG37J, ARG57Q, ARG63Q, ARG69Q, ARG91Q, ASN65Q, ASP96Q, GLN55Q, GLN58Q, GLN70Q, GLU31J, GLU43J, GLY38J, HIS40J, HIS47J, ILE142J, ILE61Q, ILE64Q, ILE93Q, ILE97Q, LEU59Q, LEU94Q, LYS102Q, LYS12J, LYS2J, LYS39J, LYS41J, LYS7J, LYS92Q, MET1J, PHE100Q, PHE4J, PHE56Q, PRO46J, THR3J, THR45J, THR5J, TRP60Q, TYR16J, TYR44J, VAL99Q
• J-R: ARG13R, ARG21R, GLN18R, HIS12R, LEU22R, LYS2J, MET1J, PHE4J, SER15R, THR19R, THR3J, TYR44J, VAL14R, VAL20R
• K-P: ALA119K, ALA41P, ALA48P, ALA57P, ARG100P, ARG102P, ARG105K, ARG108K, ARG38P, ARG61P, ARG64K, ARG70K, ARG71K, ARG71P, ARG78K, ASN65P, ASN9K, ASP73K, ASP80K, GLN40P, GLN74P, GLU101P, GLU121K, GLU33P, GLU43P, GLU67P, GLU70P, GLY101K, GLY34P, GLY66P, GLY68K, GLY68P, GLY74K, GLY81K, HIS76P, ILE116K, ILE47P, ILE63P, ILE77K, ILE99K, LEU99P, LYS36P, LYS62P, LYS66K, MET113K, PHE100K, PHE42P, PHE58P, PHE73P, PHE79K, PRO102K, PRO120K, PRO72K, PRO78P, SER35P, SER64P, SER75K, SER77P, THR103P, THR104K, THR59P, THR75P, TYR97P, VAL103K, VAL122K, VAL29P, VAL31P, VAL32P, VAL60P, VAL69K, VAL69P, VAL72P, VAL76K, VAL79P, VAL80P
• L-Q: ARG12Q, ARG18L, ARG21L, ARG5Q, GLY22L, ILE23L, ILE39Q, PHE35Q, VAL3Q
• L-R: ARG21L, ARG78R, 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, GLY553, GLY65L, GLY83, HIS233, HIS253, ILE33, ILE583, LEU283, LEU543, LEU563, LEU57L, LEU613, LEU61L, LYS113, LYS143, LYS223, LYS23, LYS243, LYS43, LYS463, LYS63L, MET483, MET55L, PHE133, PHE213, PHE50L, PHE64L, PHE66L, PRO56L, PRO623, PRO62L, SER503, THR53, TYR58L, TYR633, VAL493, VAL573, VAL63
• M-V: ALA21M, ALA35M, ALA52V, ALA54V, ALA74V, ARG18V, ARG38M, ARG79V, ASP25M, ASP76V, ASP90V, GLN51V, GLN75V, GLN78V, GLN87V, GLN97M, GLU55V, GLY37M, GLY99M, HIS80V, HIS88V, ILE89V, LEU20M, LEU61V, LEU86V, LYS100M, LYS127M, LYS133M, LYS34M, LYS53V, LYS73V, LYS83V, LYS85V, MET136M, PHE130M, PHE56V, PHE91V, PRO81V, PRO84V, PRO98M, SER58V, THR128M, THR129M, THR134M, THR24M, TYR57V, TYR82V, VAL131M, VAL135M, VAL36M, VAL77V
• M-W: GLY6W, GLY7W, GLY85M, LYS11M, LYS86M, SER8W
• M-4: LEU119M, LYS118M, LYS84
• N-P: ARG4N, SER1P
• N-S: ALA104N, ARG103N, ASN107N, ASN40S, CYS100N, GLY101N, LYS41S, LYS42S, PHE102N, THR39S, TYR38S
• N-0: ALA111N, ALA440, ALA550, ARG118N, ARG390, ARG510, ARG96N, CYS100N, GLU114N, GLU120N, GLY101N, GLY460, HIS31N, HIS370, HIS400, HIS410, ILE113N, ILE33N, ILE34N, ILE420, ILE540, ILE97N, LEU380, LEU38N, LEU98N, LYS35N, LYS520, LYS560, LYS99N, MET110N, PHE102N, PRO109N, SER119N, THR430, TYR112N, TYR470, TYR480, VAL530
• O-W: ALA46W, ALA48W, ARG13O, ARG16O, ARG40W, ASN49W, GLN19O, GLU20O, GLY47W, GLY51W, GLY72W, HIS45W, LEU21O, LYS17O, LYS61W, LYS71W, PHE78W, PRO73W, THR12O, VAL50W
• Q-R: ALA104Q, ALA107Q, ALA112Q, ALA114Q, ALA115Q, ALA3R, ALA41Q, ALA42R, ALA45Q, ALA85Q, ALA95Q, ALA98Q, ARG12Q, ARG13R, ARG47Q, ARG49Q, ARG50Q, ARG52Q, ARG63Q, ARG78R, ARG79R, ARG84R, ARG91Q, ASN43R, ASP101Q, ASP90Q, ASP96Q, GLN11R, GLN19Q, GLN36Q, GLN43Q, GLN6R, GLN86R, GLN87R, GLU110Q, GLU37R, GLU45R, GLU46R, GLU88Q, GLY42Q, GLY44R, GLY50R, GLY88R, GLY8R, GLY9R, HIS12R, HIS89R, ILE16Q, ILE39Q, ILE41R, ILE49R, ILE74R, ILE89Q, ILE93Q, ILE97Q, LEU108Q, LEU39R, LEU82Q, LEU94Q, LYS102Q, LYS10R, LYS111Q, LYS15Q, LYS40Q, LYS48R, LYS53Q, LYS73R, LYS76R, LYS84Q, LYS85R, LYS92Q, MET1R, MET40R, PHE100Q, PHE105Q, PHE35Q, PHE53R, PHE5R, PHE77R, PRO52R, SER7R, SER86Q, THR106Q, TYR2R, TYR31Q, TYR44Q, TYR46Q, TYR83R, VAL103Q, VAL109Q, VAL14R, VAL38Q, VAL47R, VAL4R, VAL51R, VAL54R, VAL72R, VAL75R, VAL87Q, VAL99Q
• Q-0: ALA26Q, ARG27Q, ARG29Q, ARG90, GLY25Q, LYS110, LYS60, MET140, SER100, SER28Q, THR80, TYR24Q, VAL30Q
• S-0: ALA200, ALA21S, ALA230, ALA43S, ALA440, ALA44S, ARG120, ARG150, ARG160, ARG18S, ARG99S, ASN40S, ASP190, ASP22S, ASP34S, GLN15S, GLN31S, GLU350, HIS180, HIS370, HIS410, ILE24S, ILE35S, ILE420, LEU19S, LEU210, LEU23S, LEU270, LEU33S, LEU36S, LEU380, LYS16S, LYS27S, LYS360, LYS41S, SER13S, SER260, SER280, SER30S, THR220, THR250, THR37S, THR39S, THR430, TYR38S, VAL17S, VAL20S, VAL240
• T-Y: ALA13T, ALA32Y, ALA33Y, ALA35T, ALA46T, ARG12T, ARG23Y, ARG29Y, ARG6T, ASN15Y, ASN27Y, GLN25Y, GLN31Y, GLN36Y, GLU17Y, GLU4T, GLU5T, GLY35Y, HIS15T, ILE30T, LEU11T, LEU14Y, LEU18Y, LEU19Y, LEU21Y, LEU22Y, LEU32T, LEU50T, LEU57Y, LEU7T, LEU8T, LYS33T, LYS49T, LYS54Y, LYS9T, MET30Y, PHE26Y, PHE51T, PRO14T, SER34Y, VAL10T, VAL16T, VAL34T, VAL47T, VAL50Y
• T-2: ARG412, ARG73T, ARG76T, ASP79T, ILE74T, LYS36T, LYS462, LYS64T
• W-3: ALA363, ARG54W, LYS383
• 1-3: GLU61, HIS303, ILE313, ILE81, LEU323, LYS343, LYS353, LYS403, LYS71, LYS91, PHE191, THR211, THR221, THR231, THR333, THR373, TYR201