3HUJ

crystal structure of human cd1d-alpha-galactosylceramide in complex with semi-invariant nkt cell receptor

• Total interactions analyzed: 28
• Total true interactions: 13
• Strongest Interaction:
  • Chains: A-B
  • Int. Res.: 131
  • Norm. En. per Res.: -3.8358
• Hub Node: A(5)

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
A-B	-85.2557	-73.9636	-343.266	-502.4853	131	16	8	12393	4	32	34
A-C	0.0	9.3834	-13.5787	-4.1953	46	0	0	1295	0	21	23
A-D	0.0	16.4376	-1.1801	15.2574	8	0	0	115	0	9	10
A-G	-14.7749	-38.2437	-117.565	-170.5836	50	13	1	4351	5	14	11
A-H	-17.4112	3.4277	-58.869	-72.8525	40	7	0	2390	1	14	15
B-C	0.0	16.8893	-4.3629	12.5264	11	0	0	197	0	10	11
B-E	-5.0869	-23.1907	-62.1461	-90.4237	35	3	0	2476	3	11	18
C-D	-59.0842	-36.9201	-335.729	-431.7332	133	14	8	12779	3	33	32
C-E	-17.7284	-35.4736	-101.26	-154.462	49	4	1	4192	5	13	11
C-F	-12.9391	3.6831	-49.8804	-59.1364	34	4	0	1901	1	14	12
D-G	-25.8518	-17.4893	-68.7501	-112.0912	33	5	0	2734	3	12	18
E-F	-79.1468	-32.9962	270.419	158.276	205	36	13	21275	5	53	40
G-H	-100.2834	-38.3522	188.326	49.6904	217	29	13	23016	11	53	46

Interface residues

• A-B: ALA100A, ALA117A, ALA15B, ALA189A, ALA19A, ALA239A, ALA30A, ARG11A, ARG12B, ARG193A, ARG246A, ARG25A, ARG3B, ARG48A, ARG97B, ASN21B, ASN238A, ASN24B, ASP122A, ASP234A, ASP240A, ASP27A, ASP34B, ASP53B, ASP59B, ASP96B, CYS12A, CYS25B, GLN119A, GLN14A, GLN2B, GLN36A, GLN8B, GLN97A, GLU241A, GLU34A, GLU50B, GLU95A, GLY120A, GLY194A, GLY210A, GLY233A, GLY28A, HIS115A, HIS13B, HIS207A, HIS31B, HIS38A, HIS51B, ILE123A, ILE15A, ILE1B, ILE235A, ILE35B, ILE7B, LEU124A, LEU13A, LEU191A, LEU203A, LEU236A, LEU23B, LEU245A, LEU29A, LEU50A, LEU54B, LEU64B, LEU65B, LEU94A, LEU96A, LYS121A, LYS186A, LYS188A, LYS214A, LYS58B, LYS6B, LYS94B, PHE113A, PHE114A, PHE118A, PHE211A, PHE22B, PHE30B, PHE56B, PHE62B, PRO14B, PRO187A, PRO195A, PRO237A, PRO32B, PRO93A, SER11B, SER125A, SER16A, SER17A, SER192A, SER209A, SER28B, SER33B, SER39A, SER41A, SER52B, SER55B, SER57B, SER61B, SER99A, THR134A, THR242A, THR68B, TRP190A, TRP23A, TRP243A, TRP31A, TRP40A, TRP60B, TRP95B, TYR10B, TYR212A, TYR244A, TYR26B, TYR63B, TYR66B, TYR67B, VAL116A, VAL185A, VAL205A, VAL208A, VAL27B, VAL85B, VAL93B, VAL98A, VAL9B
• A-C: ALA239A, ARG48A, ARG48C, ARG71A, ARG71C, ASP240A, ASP240C, ASP43A, ASP43C, ASP45A, ASP45C, ASP60A, ASP60C, GLN55A, GLN55C, GLN61C, GLN67A, GLN67C, GLU241A, GLU241C, GLU64A, GLU64C, GLY56C, LEU50A, LEU50C, LYS51A, LYS51C, PRO52A, PRO52C, SER176C, SER41A, SER41C, SER44A, SER44C, SER49A, SER49C, SER54A, SER54C, THR46A, THR46C, TRP53A, TRP53C, TRP63A, TRP63C, VAL47A, VAL47C
• A-D: ARG71A, GLN61A, GLU50D, GLU64A, HIS68A, LYS48D, PHE22D, TYR67D
• A-G: ALA144A, ALA85A, ARG103G, ARG74A, ARG79A, ARG95G, ASN149A, ASP151A, ASP80A, ASP94G, GLN146A, GLN150A, GLN2G, GLU83A, GLY100G, GLY96G, HIS68A, LEU104G, LEU143A, LEU148A, LEU88A, LEU99G, LYS152A, LYS71G, LYS82A, LYS86A, MET87A, PHE29G, PHE51G, PHE77A, PHE84A, PRO28G, SER27G, SER30G, SER52G, SER75A, SER76A, SER93G, SER97G, THR154A, THR50G, THR78A, THR98G, TRP153A, TYR105G, TYR73A, VAL147A, VAL26G, VAL72A, VAL81A
• A-H: ALA85A, ARG100H, ARG155A, ARG79A, ARG89A, ASN149A, ASN53H, ASP151A, ASP30H, ASP80A, GLN146A, GLN150A, GLU56H, GLU83A, GLY101H, GLY28H, GLY51H, GLY58H, GLY96H, HIS29H, LEU102H, LEU143A, LEU88A, LEU97H, LYS152A, LYS31H, LYS57H, LYS86A, MET87A, PHE84A, SER49H, SER54H, SER95H, THR55H, TRP153A, TYR103H, TYR48H, TYR50H, VAL147A, VAL52H
• B-C: ARG71C, ASP60C, GLN61C, GLU50B, GLU64C, GLU69B, HIS68C, LYS48B, PHE22B, THR65C, TYR67B
• B-E: ALA68E, ARG45B, ASN23E, ASN42B, ASN54E, ASP67E, ASP69E, ASP76B, CYS22E, GLN21E, GLN72E, GLU44B, GLU47B, GLU69B, GLY43B, ILE46B, LEU39B, LEU40B, LEU66E, LYS41B, LYS48B, LYS71E, PHE51E, PHE70B, SER27E, SER73E, SER74E, THR25E, THR68B, THR70E, THR71B, TYR24E, TYR78B, VAL26E, VAL49B
• C-D: ALA100C, ALA117C, ALA15D, ALA189C, ALA19C, ALA239C, ALA247C, ALA30C, ARG11C, ARG12D, ARG193C, ARG246C, ARG25C, ARG3D, ARG48C, ARG97D, ASN21D, ASN238C, ASN24D, ASP122C, ASP234C, ASP240C, ASP27C, ASP34D, ASP53D, ASP59D, ASP96D, ASP98D, CYS12C, CYS206C, CYS25D, GLN119C, GLN14C, GLN2D, GLN36C, GLN8D, GLN97C, GLU241C, GLU34C, GLU50D, GLU95C, GLY120C, GLY194C, GLY210C, GLY233C, GLY28C, HIS115C, HIS13D, HIS207C, HIS31D, HIS38C, HIS51D, ILE123C, ILE15C, ILE1D, ILE235C, ILE7D, LEU124C, LEU13C, LEU191C, LEU203C, LEU204C, LEU236C, LEU23D, LEU29C, LEU50C, LEU54D, LEU64D, LEU65D, LEU94C, LEU96C, LYS121C, LYS186C, LYS188C, LYS214C, LYS58D, LYS6D, MET99D, PHE113C, PHE114C, PHE118C, PHE18C, PHE211C, PHE22D, PHE30D, PHE56D, PHE62D, PRO14D, PRO187C, PRO195C, PRO232C, PRO237C, PRO32D, PRO93C, SER11D, SER125C, SER16C, SER17C, SER192C, SER209C, SER28D, SER33D, SER39C, SER41C, SER52D, SER55D, SER57D, SER61D, SER99C, THR134C, THR242C, THR248C, THR68D, TRP190C, TRP23C, TRP243C, TRP31C, TRP40C, TRP60D, TYR10D, TYR244C, TYR26D, TYR63D, TYR66D, TYR67D, VAL116C, VAL185C, VAL205C, VAL208C, VAL27D, VAL85D, VAL98C, VAL9D
• C-E: ALA144C, ALA85C, ARG103E, ARG79C, ARG95E, ASN149C, ASP151C, ASP80C, ASP94E, GLN146C, GLN150C, GLN2E, GLU83C, GLY100E, GLY96E, HIS68C, LEU104E, LEU143C, LEU148C, LEU88C, LEU99E, LYS152C, LYS71E, LYS82C, LYS86C, MET87C, PHE29E, PHE51E, PHE77C, PHE84C, PRO28E, SER27E, SER30E, SER52E, SER75C, SER76C, SER93E, SER97E, THR154C, THR50E, THR78C, THR98E, TRP153C, TYR105E, TYR73C, VAL147C, VAL26E, VAL72C, VAL81C
• C-F: ALA85C, ARG79C, ARG89C, ASN149C, ASN53F, ASP151C, ASP30F, ASP80C, GLN146C, GLN150C, GLU56F, GLU83C, GLY51F, GLY58F, GLY96F, LEU102F, LEU143C, LEU88C, LEU97F, LYS152C, LYS31F, LYS57F, LYS82C, LYS86C, MET87C, PHE84C, SER49F, SER54F, THR55F, TYR103F, TYR48F, TYR50F, VAL147C, VAL52F
• D-G: ALA68G, ARG45D, ASN23G, ASN42D, ASP67G, ASP69G, ASP76D, CYS22G, GLN21G, GLN72G, GLU44D, GLU47D, GLU69D, GLY43D, ILE46D, LEU39D, LEU40D, LEU66G, LYS41D, LYS48D, LYS71G, PHE29G, PHE51G, PHE70D, SER27G, SER73G, THR25G, THR68D, THR70G, THR71D, TYR24G, TYR78D, VAL49D
• E-F: ALA124E, ALA129F, ALA136F, ALA144F, ALA150F, ALA178E, ALA180E, ALA185F, ALA192F, ALA201F, ALA240F, ALA242F, ALA93F, ARG103E, ARG108E, ARG113F, ARG129E, ARG169E, ARG190F, ARG196F, ARG198F, ARG245F, ARG33E, ARG41E, ARG95E, ARG98F, ARG9F, ASN176E, ASN183E, ASN1E, ASN31E, ASP122E, ASP130E, ASP135E, ASP143E, ASP155E, ASP157E, ASP162E, ASP167E, ASP172E, ASP176F, ASP30F, ASP38E, ASP38F, ASP59F, ASP99F, CYS139E, CYS148F, CYS164E, CYS174F, CYS92F, GLN106F, GLN111E, GLN127E, GLN142F, GLN152E, GLN178F, GLN183F, GLN37E, GLN37F, GLN6F, GLN89F, GLU105F, GLU132F, GLU135F, GLU137F, GLU159F, GLU182F, GLU241F, GLU42F, GLU53E, GLY100E, GLY107E, GLY109E, GLY109F, GLY111F, GLY152F, GLY172F, GLY40E, GLY40F, GLY42E, GLY96E, GLY96F, HIS140F, HIS170F, HIS29F, HIS44F, ILE138F, ILE160E, ILE48E, ILE4F, ILE89E, LEU102F, LEU104E, LEU128E, LEU140E, LEU146F, LEU149F, LEU160F, LEU166E, LEU180F, LEU193F, LEU197F, LEU43F, LEU45F, LEU46E, LEU82E, LEU91F, LEU97F, LEU99E, LYS136E, LYS143F, LYS163E, LYS174E, LYS181F, LYS31F, LYS56E, MET168E, MET171E, MET32F, MET41F, MET49E, PHE106E, PHE108F, PHE131F, PHE141E, PHE144E, PHE173E, PHE203E, PHE203F, PHE204E, PRO110F, PRO121E, PRO123E, PRO133F, PRO177F, PRO179F, PRO184F, PRO205E, PRO39F, PRO43E, SER131E, SER134E, SER134F, SER139F, SER153E, SER156E, SER170E, SER171F, SER175E, SER177E, SER182E, SER189F, SER194F, SER195F, SER200F, SER206E, SER30E, SER45E, SER49F, SER87E, SER93E, SER94F, SER95F, SER97E, THR141F, THR142E, THR145F, THR151F, THR161E, THR175F, THR202F, THR39E, THR47E, THR50E, THR98E, TRP181E, TRP243F, TYR103F, TYR105E, TYR107F, TYR10F, TYR126E, TYR159E, TYR191F, TYR33F, TYR35E, TYR35F, TYR48F, TYR50F, VAL125E, VAL128F, VAL130F, VAL138E, VAL147F, VAL150E, VAL158E, VAL158F, VAL165E, VAL169F, VAL173F, VAL179E, VAL199F, VAL44E, VAL91E
• G-H: ALA124G, ALA129H, ALA136H, ALA144H, ALA150H, ALA178G, ALA180G, ALA185H, ALA192H, ALA201H, ALA240H, ALA242H, ALA93H, ARG100H, ARG103G, ARG108G, ARG113H, ARG129G, ARG169G, ARG190H, ARG196H, ARG198H, ARG245H, ARG33G, ARG41G, ARG95G, ARG98H, ARG9H, ASN120G, ASN176G, ASN1G, ASN31G, ASP122G, ASP130G, ASP135G, ASP143G, ASP155G, ASP157G, ASP162G, ASP167G, ASP172G, ASP176H, ASP201G, ASP30H, ASP38G, ASP59H, ASP99H, CYS139G, CYS148H, CYS164G, CYS174H, CYS189G, CYS92H, GLN106H, GLN111G, GLN127G, GLN142H, GLN152G, GLN178H, GLN183H, GLN37G, GLN37H, GLN6H, GLN89H, GLU105H, GLU132H, GLU135H, GLU137H, GLU159H, GLU182H, GLU1H, GLU241H, GLU42H, GLU53G, GLY100G, GLY101H, GLY107G, GLY109G, GLY109H, GLY111H, GLY152H, GLY172H, GLY40G, GLY40H, GLY42G, GLY96G, GLY96H, HIS140H, HIS170H, HIS29H, HIS44H, ILE118G, ILE138H, ILE160G, ILE48G, ILE89G, LEU102H, LEU104G, LEU128G, LEU140G, LEU146H, LEU149H, LEU166G, LEU180H, LEU193H, LEU197H, LEU32G, LEU43H, LEU45H, LEU82G, LEU91H, LEU97H, LEU99G, LYS132G, LYS143H, LYS154G, LYS163G, LYS174G, LYS181H, LYS31H, LYS56G, MET168G, MET171G, MET32H, MET41H, MET49G, PHE106G, PHE108H, PHE131H, PHE141G, PHE144G, PHE153H, PHE173G, PHE193G, PHE203G, PHE203H, PHE204G, PHE211H, PHE51G, PRO110H, PRO121G, PRO123G, PRO133H, PRO177H, PRO179H, PRO184H, PRO205G, PRO39H, PRO43G, SER131G, SER133G, SER134G, SER134H, SER137G, SER139H, SER153G, SER156G, SER170G, SER171H, SER175G, SER177G, SER182G, SER189H, SER194H, SER195H, SER200H, SER206G, SER30G, SER45G, SER49H, SER52G, SER87G, SER93G, SER94H, SER95H, SER97G, THR113G, THR141H, THR142G, THR145H, THR151H, THR161G, THR175H, THR39G, THR47G, THR50G, THR55G, THR98G, TRP181G, TRP204H, TRP243H, TYR103H, TYR105G, TYR107H, TYR10H, TYR126G, TYR159G, TYR191H, TYR33H, TYR35G, TYR35H, TYR48H, TYR50H, VAL125G, VAL128H, VAL130H, VAL138G, VAL147H, VAL150G, VAL158G, VAL165G, VAL169H, VAL173H, VAL179G, VAL199H, VAL44G, VAL91G