2QBK

crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin and ribosome recycling factor (rrf). this file contains the 50s subunit of the second 70s ribosome, with gentamicin and rrf bound. the entire crystal structure contains two 70s ribosomes and is described in remark 400.

• Total interactions analyzed: 496
• Total true interactions: 29
• Strongest Interaction:
  • Chains: K-P
  • Int. Res.: 81
  • Norm. En. per Res.: -4.0477
• 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-K	-10.2503	-7.6818	-31.1731	-49.1052	18	3	0	1083	0	2	6
D-P	0.0	6.8962	-135.542	-128.6458	59	11	3	6118	1	13	13
D-J	0.0	3.0518	-22.6221	-19.5703	11	0	1	954	0	0	6
D-N	-11.8112	2.2123	-22.5654	-32.1643	17	9	0	1301	0	0	9
K-P	-46.2798	-89.794	-191.788	-327.8619	81	16	3	7559	5	33	32
E-2	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	0	0
E-L	-3.2863	0.0	-123.02	-126.3063	45	8	5	5894	0	9	8
E-Q	0.0	0.0	-0.7907	-0.7907	6	0	0	159	0	0	3
0-N	0.0	3.7115	-68.407	-64.6954	40	4	4	3339	0	9	19
0-Q	0.0	19.6073	-20.8947	-1.2874	15	0	0	815	0	0	7
0-S	-12.7132	-10.4926	-79.1458	-102.3516	50	7	6	3606	2	10	8
4-M	0.0	0.0	-0.0506	-0.0506	3	0	0	30	0	0	1
4-G	0.0	0.0	-2.4209	-2.4209	11	0	0	263	0	2	5
1-3	0.0	1.5153	-17.9686	-16.4533	18	5	0	1108	0	1	8
3-L	-8.551	37.8755	-187.894	-158.5695	59	5	5	8274	0	5	33
3-W	0.0	0.0	-0.0486	-0.0486	3	0	0	28	0	1	2
V-M	-2.5377	-7.0752	-79.6644	-89.2774	52	13	4	3744	0	4	11
2-T	0.0	0.0	-0.0067	-0.0067	3	0	0	6	0	1	4
L-Q	0.0	0.0	-0.0085	-0.0085	6	0	0	12	0	0	2
L-R	0.0	2.8748	-31.7977	-28.923	24	4	0	1439	0	0	12
M-W	0.0	0.0	-0.0695	-0.0695	7	0	0	33	0	0	0
M-6	0.0	-13.7814	-4.8256	-18.6071	11	0	0	421	0	10	5
X-T	-10.8957	10.0015	-66.9699	-67.864	44	9	1	4082	0	10	18
H-Z	0.0	-21.1207	-43.7198	-64.8405	34	9	0	2137	1	8	12
J-Q	0.0	-0.2623	-72.9464	-73.2087	45	8	7	4488	0	10	20
J-R	0.0	0.0	-2.3515	-2.3515	11	0	0	391	0	0	4
N-S	-9.7627	0.0	-7.5701	-17.3328	13	7	0	483	0	2	2
O-W	0.0	-1.8709	-1.4783	-3.3492	19	0	0	284	0	5	9
Q-R	-31.3413	-6.9559	-244.5	-282.7972	102	68	7	11444	2	21	55

Interface residues

• D-K: ARG128D, ARG13D, ARG31K, ARG70K, ARG71K, ASP18D, ASP73K, GLY19D, GLY74K, HIS29K, ILE22D, PHE15D, PRO23D, PRO72K, SER21D, SER75K, THR16D, VAL20D
• 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, LYS5P, LYS7D, LYS8D, MET11D, MET12P, PHE15D, PHE73P, PRO23D, PRO78P, SER1P, SER21D, SER56P, SER77P, THR12D, THR16D, THR197D, THR25D, THR75P, TRP30P, VAL178D, VAL20D, VAL24D, VAL26D, VAL32P, VAL79P, VAL80P, VAL9D
• D-J: GLY158D, GLY79J, GLY82J, HIS77J, HIS80J, ILE81J, LYS154D, LYS157D, LYS159D, PHE156D, THR78J
• D-N: ALA119D, ALA196D, ARG2N, ARG4N, ASN167D, GLN164D, GLY115D, GLY117D, GLY166D, HIS3N, LYS114D, LYS116D, LYS123D, MET165D, MET1N, PHE118D, THR197D
• K-P: ALA119K, ALA11K, ALA41P, ALA48P, ALA57P, ALA83K, ARG100P, 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, ILE116K, ILE47P, ILE63P, ILE77K, ILE99K, LEU118K, LYS36P, LYS62P, LYS66K, MET113K, PHE100K, PHE42P, PHE58P, PHE73P, PHE79K, PRO102K, PRO120K, PRO72K, PRO78P, SER35P, SER64P, SER75K, SER77P, THR104K, THR59P, THR65K, THR75P, TRP30P, TYR97P, VAL103K, VAL10K, VAL122K, VAL29P, VAL31P, VAL32P, VAL60P, VAL63K, VAL69K, VAL69P, VAL72P, VAL76K, VAL79P, VAL80P
• E-2: LYS372, SER55E
• E-L: ALA104E, ALA182E, ALA26E, ALA9L, ARG114E, ARG117E, ARG21L, ARG2L, ASN24E, ASN4L, ASP184E, GLN115E, GLN30E, GLN94E, GLU10L, GLU111E, GLU25E, HIS29E, ILE108E, ILE181E, 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
• 0-N: ALA111N, ALA440, ALA550, ARG118N, ARG390, ARG490, ARG510, ARG96N, CYS100N, GLU114N, GLU120N, GLY101N, GLY460, HIS370, HIS400, HIS410, ILE113N, ILE33N, ILE34N, ILE420, ILE540, ILE97N, LEU115N, LEU380, LEU38N, LEU98N, LYS35N, LYS520, LYS560, LYS99N, MET110N, PHE102N, PRO109N, SER119N, THR430, TYR112N, TYR470, TYR480, VAL116N, VAL530
• 0-Q: ALA26Q, ARG120, ARG27Q, ARG29Q, ARG90, GLY25Q, LYS110, LYS60, MET140, PRO70, SER100, SER28Q, THR80, TYR24Q, VAL30Q
• 0-S: ALA14S, ALA200, ALA21S, ALA230, ALA43S, ALA440, ALA44S, ARG120, ARG150, ARG160, ARG18S, ARG390, ARG99S, ASN40S, ASP190, ASP22S, ASP34S, GLN15S, GLN31S, GLU350, GLU78S, GLY130, HIS180, HIS370, HIS410, ILE24S, ILE35S, LEU19S, LEU210, LEU23S, LEU270, LEU33S, LEU36S, LEU380, LYS16S, LYS27S, LYS360, LYS41S, SER260, SER280, SER30S, THR220, THR250, THR37S, THR39S, THR430, TYR38S, VAL17S, VAL20S, VAL240
• 4-M: LYS118M, LYS84, LYS94
• 4-G: ALA294, ARG169G, ASN134, CYS274, GLU304, LYS171G, LYS324, PRO155G, PRO314, SER284, VAL167G
• 1-3: ARG443, GLU61, ILE313, ILE81, LEU323, LYS343, LYS353, LYS371, LYS403, LYS71, LYS91, PRO401, THR211, THR221, THR231, THR333, THR373, TYR201
• 3-L: ALA103, ALA263, ALA473, ALA593, ALA93, ARG123, ARG293, ARG47L, ARG48L, ARG59L, ARG60L, ARG73, ASN273, ASP533, CYS603, GLU51L, GLY49L, GLY523, GLY52L, GLY553, GLY65L, GLY83, HIS233, HIS253, ILE33, ILE583, LEU283, LEU433, LEU543, LEU563, LEU57L, LEU613, LEU61L, LYS113, LYS143, LYS223, LYS243, LYS43, LYS463, LYS513, LYS63L, MET483, MET55L, PHE133, PHE213, PHE50L, PHE64L, PHE66L, PRO56L, PRO623, PRO62L, SER503, THR53, THR67L, TYR58L, TYR633, VAL493, VAL573, VAL63
• 3-W: ALA363, ARG54W, LYS383
• V-M: ALA21M, ALA35M, ALA52V, ALA54V, ALA74V, ARG18V, ARG79V, ASP25M, ASP76V, ASP90V, GLN22M, GLN51V, GLN75V, GLN78V, GLN87V, GLN97M, GLU55V, GLY19M, GLY37M, GLY99M, HIS80V, HIS88V, ILE89V, LEU20M, LEU61V, LEU86V, LYS100M, LYS127M, LYS133M, LYS34M, LYS53V, LYS83V, LYS85V, MET136M, PHE130M, PHE56V, PHE91V, PRO81V, PRO84V, PRO98M, SER58V, THR128M, THR129M, THR132M, THR134M, THR24M, TYR57V, TYR82V, VAL131M, VAL135M, VAL36M, VAL77V
• 2-T: ARG412, ARG73T, ILE74T
• L-Q: ARG12Q, ARG21L, ARG5Q, GLY22L, ILE23L, PHE35Q
• L-R: ARG21L, ARG78R, ARG80R, ARG84R, GLN86R, GLY20L, GLY22L, GLY24L, GLY26L, GLY28L, GLY31L, GLY32L, HIS35L, HIS82R, ILE23L, LEU27L, LYS29L, LYS76R, LYS81R, LYS85R, PHE77R, SER25L, THR30L, TYR83R
• M-W: ARG10M, GLY6W, GLY85M, LYS11M, LYS84M, LYS86M, SER8W
• M-6: ALA79M, ARG1566, ARG81M, ASP1526, GLU1516, GLU1536, LEU78M, LYS84M, PRO77M, SER1506, VAL80M
• X-T: ALA13T, ALA32X, ALA33X, ALA35T, ALA46T, ARG12T, ARG23X, ARG29X, ARG6T, ASN27X, GLN25X, GLN31X, GLN48T, GLU17X, GLU4T, GLU52T, GLU5T, GLY35X, HIS15T, LEU11T, LEU14X, LEU18X, LEU21X, LEU22X, LEU28X, LEU32T, LEU43X, LEU50T, LEU7T, LEU8T, LYS33T, LYS49T, LYS54X, LYS9T, MET1T, MET30X, PHE26X, PHE51T, PRO14T, SER34X, VAL10T, VAL34T, VAL47T, VAL50X
• H-Z: ALA23H, ALA26H, ALA39H, ARG27H, ARG37Z, ARG57Z, ASN28H, ASN43H, ASP60Z, ASP65Z, GLN33H, GLU41Z, GLY24H, GLY34H, GLY63Z, HIS36Z, ILE59Z, ILE64Z, LYS41H, LYS61Z, LYS62Z, MET1H, MET56Z, PHE38Z, PHE46Z, PRO32H, PRO38H, THR40H, TRP39Z, VAL31H, VAL3H, VAL40Z, VAL58Z, VAL67Z
• J-Q: ALA42J, ALA62Q, ALA66Q, ALA67Q, ALA68Q, ALA6J, ALA95Q, ALA98Q, ARG34J, ARG35J, ARG37J, ARG63Q, ARG69Q, ASN65Q, ASP96Q, GLN55Q, GLN58Q, GLN70Q, 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, PHE4J, SER15R, THR19R, THR3J, VAL14R, VAL20R
• N-S: ALA108N, ARG103N, ASN107N, ASN40S, ASP106N, GLY101N, LYS41S, LYS42S, PHE102N, PRO109N, THR37S, THR39S, TYR38S
• O-W: ALA46W, ALA48W, ARG13O, ARG16O, ARG40W, ASN49W, GLN19O, GLU20O, GLY47W, GLY51W, GLY72W, HIS45W, LEU21O, 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, ARG63Q, ARG78R, ARG79R, ARG84R, ARG91Q, ASP101Q, ASP90Q, ASP96Q, GLN11R, GLN19Q, GLN36Q, GLN43Q, GLN6R, GLN86R, GLN87R, GLN91R, GLU110Q, GLU37R, GLU45R, GLU46R, GLU88Q, GLY42Q, GLY44R, GLY50R, GLY81Q, GLY88R, GLY8R, GLY9R, HIS12R, HIS89R, ILE16Q, ILE39Q, ILE41R, ILE49R, ILE74R, ILE89Q, ILE93Q, ILE97Q, LEU108Q, LEU39R, LEU82Q, LEU94Q, LYS102Q, LYS10R, LYS111Q, LYS113Q, LYS15Q, LYS40Q, LYS48R, LYS53Q, LYS73R, LYS76R, LYS83Q, LYS84Q, LYS85R, LYS92Q, 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