2I2V

crystal structure of ribosome with messenger rna and the anticodon stem-loop of p-site trna. 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: 28
• Strongest Interaction:
  • Chains: K-P
  • Int. Res.: 74
  • Norm. En. per Res.: -3.2442
• 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	3.6282	-25.954	-22.3258	12	1	1	1029	0	0	7
D-K	-9.7906	-8.0696	-26.858	-44.7182	20	2	0	1054	0	3	6
D-N	-14.0094	1.9741	-26.5863	-38.6216	17	10	0	1172	0	0	9
D-P	-7.835	9.7473	-142.32	-140.4077	61	17	5	6472	1	13	12
E-L	0.0	0.0	-100.539	-100.539	46	18	4	5425	1	9	6
E-Q	0.0	0.0	-0.1172	-0.1172	6	0	0	53	0	0	2
E-2	0.0	0.0	-0.0037	-0.0037	3	0	0	4	0	0	0
G-4	-6.1661	-7.6776	-7.3223	-21.166	9	0	0	309	0	2	4
H-X	0.0	-15.0265	-40.5062	-55.5327	35	4	0	2058	0	8	12
J-Q	0.0	-2.1536	-95.4077	-97.5613	46	16	7	4967	0	10	23
J-R	0.0	0.0	-3.3145	-3.3145	13	0	0	585	0	1	4
K-P	-46.5526	-25.9444	-167.571	-240.068	74	13	3	6949	3	30	34
L-Q	0.0	0.0	-0.0048	-0.0048	6	0	0	8	0	0	2
L-R	0.0	2.5709	-34.6189	-32.048	24	4	1	1576	0	0	13
L-3	0.0	19.974	-189.891	-169.917	61	13	5	8276	0	4	32
M-V	-6.2819	-5.3737	-93.4639	-105.1194	52	4	4	3858	0	5	12
M-W	0.0	0.0	-0.2858	-0.2858	7	0	0	63	0	0	0
M-4	0.0	0.0	-0.0022	-0.0022	3	0	0	3	0	1	1
N-S	0.0	0.0	-14.0185	-14.0185	12	3	0	417	0	2	2
N-0	0.0	3.0317	-60.731	-57.6993	37	6	3	3144	0	13	19
O-W	0.0	-4.5022	-1.8144	-6.3166	20	0	0	283	0	4	5
Q-R	-21.7016	-6.5709	-240.857	-269.1295	100	50	9	11597	0	23	52
Q-0	0.0	0.0	-11.3331	-11.3331	13	5	0	718	0	0	5
S-0	-16.9419	-18.1857	-95.053	-130.1806	51	12	9	4161	2	10	7
T-Y	0.0	22.1297	-73.3293	-51.1996	46	14	1	3749	0	9	16
T-2	0.0	0.0	-0.0004	-0.0004	2	0	0	1	0	1	4
W-3	0.0	0.0	-0.0012	-0.0012	2	0	0	3	0	1	2
1-3	0.0	1.1121	-18.2619	-17.1498	20	4	0	1129	0	1	8

Interface residues

• D-J: GLY158D, GLY79J, GLY82J, HIS77J, HIS80J, ILE81J, LYS154D, LYS157D, LYS159D, LYS160D, PHE156D, THR78J
• D-K: ARG128D, ARG13D, ARG30K, ARG69K, ARG70K, ASP18D, ASP72K, GLY19D, GLY73K, HIS28K, ILE14D, ILE22D, LYS190D, PHE15D, PRO23D, PRO71K, SER21D, SER74K, 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, GLY198D, 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, VAL178D, VAL20D, VAL24D, VAL26D, VAL32P, VAL79P, VAL80P, VAL9D
• E-L: ALA182E, ALA26E, ALA36E, ALA9L, ARG114E, ARG117E, ARG21L, ARG2L, ASN24E, ASN4L, ASP184E, GLN115E, GLN30E, GLN94E, GLU10L, GLU111E, GLU25E, HIS29E, ILE108E, ILE181E, LEU109E, LEU112E, LEU180E, LEU27E, LEU3L, LEU6L, LYS13L, LYS166E, 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: GLY54E, LYS372, THR53E
• G-4: ALA294, ARG169G, CYS274, GLU304, LYS324, PRO155G, PRO314, SER284, VAL167G
• H-X: ALA23H, ALA26H, ARG27H, ARG36X, ARG44X, ARG56X, ASN28H, ASP59X, ASP64X, GLN33H, GLU40X, GLY24H, GLY34H, GLY62X, HIS35X, ILE58X, ILE63X, LYS41H, LYS43X, LYS60X, LYS61X, MET1H, MET55X, PHE37X, PHE45X, PRO32H, PRO38H, SER41X, THR40H, THR65X, TRP38X, VAL31H, VAL39X, VAL3H, VAL57X
• J-Q: ALA42J, ALA62Q, ALA66Q, ALA67Q, ALA6J, ALA95Q, ALA98Q, ARG34J, ARG35J, ARG57Q, ARG63Q, ARG69Q, ARG91Q, ASN65Q, ASP96Q, GLN55Q, GLN58Q, GLN70Q, GLU43J, GLY38J, HIS40J, HIS47J, ILE61Q, ILE64Q, ILE93Q, LEU59Q, LEU94Q, LYS102Q, LYS12J, LYS2J, LYS39J, LYS41J, LYS92Q, MET1J, PHE100Q, PHE4J, PHE56Q, PRO46J, THR3J, THR45J, THR5J, TRP60Q, TYR16J, TYR44J, VAL48J, VAL99Q
• J-R: ARG13R, ARG21R, GLN11R, GLN18R, HIS12R, LYS2J, MET1J, PHE4J, SER15R, THR19R, THR3J, VAL14R, VAL20R
• K-P: ALA118K, ALA41P, ALA57P, ALA82K, ARG100P, ARG104K, ARG107K, ARG38P, ARG61P, ARG63K, ARG69K, ARG70K, ARG71P, ARG77K, ASN65P, ASN8K, ASP72K, ASP79K, GLN40P, GLN74P, GLU101P, GLU120K, GLU33P, GLU67P, GLU70P, GLY100K, GLY34P, GLY66P, GLY67K, GLY68P, GLY73K, GLY80K, HIS76P, ILE115K, ILE47P, ILE63P, ILE76K, ILE98K, LEU117K, LYS36P, LYS62P, LYS65K, LYS66K, MET112K, PHE42P, PHE58P, PHE73P, PHE78K, PHE99K, PRO101K, PRO119K, PRO71K, PRO78P, SER35P, SER56P, SER64P, SER74K, SER77P, THR103K, THR59P, THR75P, TYR97P, VAL102K, VAL121K, VAL29P, VAL31P, VAL32P, VAL60P, VAL68K, VAL69P, VAL72P, VAL75K, VAL79P, VAL80P
• 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
• L-3: ALA103, ALA263, ALA473, ALA593, ALA93, ARG123, ARG293, ARG47L, ARG48L, ARG59L, ARG60L, ARG73, ASN273, ASP533, CYS603, GLN54L, GLU51L, GLY49L, GLY523, GLY52L, GLY553, GLY65L, GLY83, HIS233, HIS253, ILE33, ILE583, LEU283, LEU433, LEU543, LEU563, LEU57L, LEU613, LEU61L, LYS113, LYS143, LYS153, LYS223, LYS243, LYS43, LYS463, LYS513, LYS63L, MET483, MET55L, PHE133, PHE213, PHE50L, PHE64L, PHE66L, PRO56L, PRO623, PRO62L, SER503, THR53, THR67L, TYR58L, TYR633, VAL493, VAL573, VAL63
• M-V: ALA21M, ALA35M, ALA52V, ALA54V, ALA74V, ARG18V, ARG38M, ARG79V, ASP25M, ASP76V, ASP90V, GLN51V, GLN75V, GLN78V, GLN87V, GLN97M, GLU55V, GLY19M, GLY37M, GLY99M, HIS80V, HIS88V, ILE89V, LEU20M, LEU61V, LYS100M, LYS127M, LYS133M, LYS34M, LYS53V, LYS73V, LYS83V, LYS85V, MET136M, PHE130M, PHE56V, PHE91V, PRO81V, PRO84V, PRO98M, SER58V, THR128M, THR129M, THR134M, THR24M, TYR57V, TYR82V, VAL131M, VAL135M, VAL26M, VAL36M, VAL77V
• M-W: GLY6W, GLY7W, GLY85M, LYS11M, LYS84M, LYS86M, SER8W
• M-4: GLU115M, LYS118M, LYS84
• N-S: ALA104N, ALA108N, ARG103N, ASN107N, ASN40S, CYS100N, LYS41S, LYS42S, PHE102N, THR37S, THR39S, TYR38S
• N-0: ALA111N, ALA550, ARG118N, ARG390, ARG490, ARG510, ARG96N, CYS100N, GLU114N, GLU32N, GLY101N, GLY460, HIS370, HIS400, HIS410, ILE113N, ILE33N, ILE34N, ILE420, ILE540, ILE97N, LEU115N, LEU380, LEU38N, LEU98N, LYS520, LYS560, LYS99N, MET110N, PHE102N, SER119N, THR430, TYR112N, TYR470, TYR480, VAL116N, 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, 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, GLU37R, GLU45R, GLU46R, GLU70R, GLU88Q, GLY42Q, GLY44R, GLY50R, GLY8R, GLY9R, HIS12R, HIS89R, ILE16Q, ILE39Q, ILE41R, ILE49R, ILE74R, ILE89Q, ILE93Q, ILE97Q, LEU108Q, LEU39R, LEU82Q, LEU94Q, LYS102Q, LYS10R, LYS111Q, LYS15Q, LYS18Q, LYS40Q, LYS48R, LYS73R, LYS76R, LYS83Q, LYS84Q, LYS85R, LYS92Q, MET40R, PHE100Q, PHE105Q, PHE35Q, PHE53R, PHE5R, PHE77R, PRO52R, SER7R, SER86Q, THR106Q, TRP60Q, TYR2R, TYR31Q, TYR44Q, TYR46Q, TYR83R, VAL103Q, VAL109Q, VAL14R, VAL20R, VAL38Q, VAL47R, VAL4R, VAL51R, VAL54R, VAL72R, VAL75R, VAL87Q, VAL99Q
• Q-0: ALA26Q, ARG120, ARG27Q, ARG29Q, ARG90, GLY25Q, LYS110, LYS60, SER100, SER28Q, THR80, TYR24Q, VAL30Q
• S-0: 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, 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-Y: ALA13T, ALA32Y, ALA33Y, ALA35T, ALA46T, ARG12T, ARG23Y, ARG29Y, ARG47Y, ARG6T, ASN15Y, ASN27Y, GLN25Y, GLN31Y, GLU17Y, GLU4T, GLU52T, GLU5T, GLY35Y, HIS15T, ILE30T, LEU11T, LEU14Y, LEU18Y, LEU19Y, LEU21Y, LEU22Y, LEU32T, LEU43Y, LEU50T, LEU57Y, LEU7T, LEU8T, LYS33T, LYS49T, LYS54Y, LYS9T, MET30Y, PHE26Y, PHE51T, PRO14T, SER34Y, VAL10T, VAL16T, VAL34T, VAL47T
• T-2: ARG412, ARG73T
• W-3: ARG54W, LYS383
• 1-3: ARG443, GLU61, HIS303, ILE313, ILE81, LEU323, LYS343, LYS353, LYS371, LYS403, LYS71, LYS91, PHE191, PRO401, THR211, THR221, THR231, THR333, THR373, TYR201