3IKM

crystal structure of human mitochondrial dna polymerase holoenzyme

• Total interactions analyzed: 15
• Total true interactions: 8
• Strongest Interaction:
  • Chains: E-F
  • Int. Res.: 207
  • Norm. En. per Res.: -2.6825
• Hub Node: B(3)

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	0.0	-11.9098	-4.3073	-16.2171	23	0	0	293	2	10	6
A-C	-76.0952	-192.1176	-239.677	-507.8898	241	117	8	21236	11	98	108
B-C	-93.2036	-127.4038	-315.429	-536.0364	218	113	5	20119	10	66	76
B-D	0.0	0.0	-1.7952	-1.7952	14	0	0	121	0	2	3
B-E	0.0	14.855	-0.8877	13.9673	5	0	0	65	0	4	4
D-E	-3.9608	0.0	-6.6958	-10.6566	33	0	0	558	1	15	4
D-F	-77.5886	-114.4214	-253.424	-445.4339	233	156	3	20709	8	92	107
E-F	-98.4608	-126.5761	-330.233	-555.2699	207	124	8	18122	11	63	73

Interface residues

• A-B: ALA510A, ARG122B, ARG232A, ARG257B, ASN484B, ASP243A, ASP542A, GLN238A, GLN540A, GLN541A, GLU394B, GLU449B, GLU535A, GLU537A, GLU538A, LEU448B, LYS470B, PHE121B, PHE254B, PHE539A, TRP251B, TYR233A, VAL398B
• A-C: ALA267C, ALA467A, ALA470A, ALA482C, ALA545A, ALA547A, ALA604A, ALA710A, ALA718A, ALA781A, ALA786A, ARG1208A, ARG1209A, ARG246C, ARG257C, ARG264C, ARG284C, ARG363C, ARG369C, ARG396C, ARG443A, ARG456C, ARG457A, ARG458C, ARG546A, ARG574A, ARG790A, ARG869A, ASN1202A, ASN249C, ASN272C, ASN287C, ASN292C, ASN359C, ASN404C, ASN409C, ASN440A, ASN450C, ASN468A, ASN484C, ASP253C, ASP277C, ASP326C, ASP459C, ASP465A, ASP469A, ASP473C, ASP487A, ASP491A, ASP542A, ASP830A, ASP832A, CYS278C, CYS377C, CYS399C, CYS471A, CYS548A, CYS577A, GLN250C, GLN261C, GLN279C, GLN355C, GLN397C, GLN400C, GLN439A, GLN472A, GLN493A, GLN540A, GLN541A, GLN550A, GLN666A, GLN715A, GLU1207A, GLU358C, GLU394C, GLU405C, GLU408C, GLU447A, GLU449C, GLU454A, GLU458A, GLU464C, GLU489A, GLU494A, GLU537A, GLU538A, GLU557A, GLU662A, GLU834A, GLY1205A, GLY1211A, GLY286C, GLY401C, GLY450A, GLY451C, GLY476A, GLY554A, GLY571A, GLY714A, GLY782A, GLY784A, GLY785A, GLY788A, HIS258C, HIS368C, HIS375C, HIS454C, HIS467C, HIS565A, HIS569A, HIS613A, ILE453C, ILE468C, ILE476C, ILE479C, ILE794A, LEU252C, LEU256C, LEU260C, LEU303C, LEU356C, LEU367C, LEU385C, LEU393C, LEU395C, LEU402C, LEU406C, LEU407C, LEU438C, LEU448C, LEU452C, LEU455A, LEU466A, LEU471C, LEU473A, LEU474A, LEU475C, LEU488A, LEU549A, LEU552A, LEU558A, LEU559A, LEU566A, LEU576A, LEU602A, LEU605A, LEU717A, LYS1198A, LYS265C, LYS285C, LYS288C, LYS364C, LYS365C, LYS370C, LYS373C, LYS461A, LYS463C, LYS470C, LYS472C, LYS477C, LYS483C, LYS496A, LYS551A, LYS553A, LYS561A, LYS575A, LYS601A, LYS665A, MET1206A, MET268C, MET459A, MET462C, MET464A, MET465C, MET466C, MET544A, MET603A, MET669A, MET797A, PHE254C, PHE266C, PHE361C, PHE403C, PHE439C, PHE474C, PRO1203A, PRO270C, PRO376C, PRO483A, PRO560A, PRO570A, PRO578A, PRO600A, PRO670A, PRO716A, PRO783A, PRO789A, SER1201A, SER248C, SER269C, SER271C, SER275C, SER276C, SER360C, SER462A, SER469C, SER475A, SER480C, SER481C, SER787A, THR1204A, THR357C, THR362C, THR446C, THR447C, THR451A, THR460C, THR461C, THR555A, THR556A, THR606A, TRP251C, TRP255C, TRP263C, TRP304C, TRP484A, TRP486A, TRP572A, TRP607A, TYR1210A, TYR417C, TYR444A, TYR478C, TYR479A, TYR573A, TYR831A, VAL371C, VAL398C, VAL443C, VAL485C, VAL543A
• B-C: ALA111C, ALA112B, ALA112C, ALA130B, ALA130C, ALA209B, ALA209C, ARG107B, ARG107C, ARG122B, ARG122C, ARG182B, ARG182C, ARG203B, ARG203C, ARG325C, ARG328C, ARG396B, ARG75B, ARG75C, ARG76B, ARG76C, ASN109C, ASN195B, ASN195C, ASN201B, ASN201C, ASN404B, ASN404C, ASP129B, ASP129C, ASP198B, ASP198C, ASP326C, ASP343B, ASP343C, ASP386B, CYS196B, CYS196C, CYS214B, CYS214C, CYS399B, CYS95B, CYS95C, GLN124B, GLN124C, GLN210B, GLN210C, GLN397B, GLN400B, GLN422C, GLN74B, GLN74C, GLN85C, GLU105B, GLU105C, GLU123B, GLU123C, GLU191B, GLU191C, GLU233B, GLU233C, GLU408B, GLU408C, GLU419B, GLU419C, GLY100B, GLY100C, GLY103B, GLY103C, GLY136B, GLY136C, GLY212B, GLY212C, GLY232B, GLY232C, GLY327C, GLY401B, GLY410B, GLY410C, GLY416B, GLY81B, GLY81C, GLY94B, GLY94C, GLY98B, GLY98C, HIS132B, HIS132C, HIS133B, HIS133C, HIS192B, HIS192C, HIS77B, HIS77C, HIS96B, HIS96C, ILE211B, ILE211C, ILE231B, ILE231C, ILE381B, ILE381C, ILE411C, LEU102B, LEU102C, LEU106B, LEU106C, LEU131B, LEU131C, LEU181B, LEU181C, LEU197B, LEU197C, LEU199B, LEU199C, LEU204C, LEU208B, LEU208C, LEU393B, LEU407B, LEU407C, LEU418B, LEU418C, LEU428B, LEU79B, LEU79C, LYS108B, LYS108C, LYS134B, LYS134C, LYS180C, LYS202B, LYS202C, LYS229C, LYS234B, LYS234C, LYS431B, LYS431C, LYS483C, MET346B, MET421B, MET421C, MET435B, PHE121B, PHE121C, PHE126B, PHE126C, PHE215B, PHE215C, PHE403B, PHE403C, PHE78B, PHE78C, PHE99B, PHE99C, PRO101B, PRO101C, PRO127B, PRO127C, PRO135B, PRO135C, PRO205C, PRO217B, PRO380B, PRO380C, PRO415B, PRO415C, PRO97B, PRO97C, SER117C, SER230B, SER230C, SER412B, SER412C, SER423B, SER423C, SER80B, SER80C, SER82B, SER82C, SER93B, THR116B, THR116C, THR235B, THR235C, THR420B, TRP114C, TRP115B, TRP115C, TRP414B, TRP414C, TYR193C, TYR206B, TYR206C, TYR417B, TYR417C, VAL104B, VAL104C, VAL118C, VAL119B, VAL119C, VAL120B, VAL120C, VAL125B, VAL125C, VAL128B, VAL128C, VAL194B, VAL194C, VAL200B, VAL200C, VAL213B, VAL213C, VAL387B, VAL398B, VAL413B, VAL413C
• B-D: ARG227D, ARG369B, ARG386D, ARG389B, GLN226D, GLN422B, GLN427B, GLU230D, GLU426B, LYS370B, SER424B, SER430B, TRP169D, TRP171D
• B-E: GLU445E, GLU449B, GLU449E, THR446B, THR446E
• D-E: ARG122E, ARG232D, ARG257E, ARG546D, ASN450E, ASN484E, ASP243D, ASP542D, GLN238D, GLN261E, GLN397E, GLN540D, GLN541D, GLU394E, GLU449E, GLU535D, GLU536D, GLU537D, GLU538D, HIS258E, LEU448E, LYS265E, PHE121E, PHE254E, PHE539D, SER240D, SER480E, SER481E, SER534D, TRP251E, TYR233D, VAL120E, VAL485E
• D-F: ALA267F, ALA467D, ALA470D, ALA482F, ALA545D, ALA547D, ALA604D, ALA710D, ALA711D, ALA786D, ARG1208D, ARG1209D, ARG246F, ARG257F, ARG264F, ARG284F, ARG363F, ARG369F, ARG396F, ARG443D, ARG457D, ARG458F, ARG546D, ARG574D, ARG579D, ARG709D, ARG790D, ASN1202D, ASN249F, ASN272F, ASN287F, ASN292F, ASN305F, ASN359F, ASN366F, ASN404F, ASN409F, ASN440D, ASN450F, ASN468D, ASN484F, ASP253F, ASP277F, ASP326F, ASP433F, ASP459F, ASP465D, ASP469D, ASP473F, ASP487D, ASP491D, ASP542D, ASP830D, ASP832D, CYS399F, CYS471D, CYS548D, CYS577D, GLN250F, GLN261F, GLN355F, GLN397F, GLN400F, GLN439D, GLN472D, GLN493D, GLN540D, GLN541D, GLN550D, GLN666D, GLN715D, GLU1207D, GLU358F, GLU394F, GLU405F, GLU408F, GLU447D, GLU449F, GLU454D, GLU458D, GLU464F, GLU494D, GLU537D, GLU538D, GLU557D, GLU662D, GLU672D, GLU793D, GLU834D, GLY1205D, GLY1211D, GLY286F, GLY401F, GLY450D, GLY451F, GLY476D, GLY554D, GLY571D, GLY714D, GLY782D, GLY784D, GLY785D, GLY788D, HIS258F, HIS368F, HIS375F, HIS454F, HIS467F, HIS569D, HIS613D, ILE453F, ILE468F, ILE479F, ILE515D, ILE794D, LEU252F, LEU256F, LEU260F, LEU303F, LEU356F, LEU367F, LEU385F, LEU393F, LEU395F, LEU402F, LEU406F, LEU407F, LEU438F, LEU448F, LEU452F, LEU455D, LEU466D, LEU471F, LEU473D, LEU474D, LEU488D, LEU549D, LEU552D, LEU558D, LEU559D, LEU566D, LEU576D, LEU602D, LEU717D, LYS1198D, LYS265F, LYS285F, LYS364F, LYS365F, LYS370F, LYS373F, LYS461D, LYS463F, LYS470F, LYS472F, LYS477F, LYS483F, LYS496D, LYS551D, LYS553D, LYS561D, LYS575D, MET1206D, MET268F, MET462F, MET464D, MET465F, MET466F, MET544D, MET603D, MET669D, MET797D, PHE254F, PHE266F, PHE273F, PHE361F, PHE403F, PHE439F, PHE474F, PRO1203D, PRO270F, PRO376F, PRO560D, PRO570D, PRO578D, PRO670D, PRO783D, PRO789D, SER1201D, SER248F, SER269F, SER271F, SER275F, SER276F, SER337F, SER360F, SER462D, SER469F, SER475D, SER480F, SER481F, SER787D, THR1204D, THR247F, THR357F, THR362F, THR446F, THR447F, THR451D, THR460F, THR461F, THR555D, THR556D, TRP251F, TRP255F, TRP262F, TRP263F, TRP304F, TRP484D, TRP572D, TYR1210D, TYR417F, TYR444D, TYR478F, TYR479D, TYR573D, TYR831D, VAL371F, VAL398F, VAL443F, VAL485F, VAL543D, VAL712D
• E-F: ALA112E, ALA112F, ALA130E, ALA130F, ALA209E, ALA209F, ALA384F, ARG107E, ARG107F, ARG122E, ARG122F, ARG182E, ARG182F, ARG203E, ARG203F, ARG325F, ARG328E, ARG396E, ARG75E, ARG75F, ARG76E, ARG76F, ASN195E, ASN195F, ASN201E, ASN201F, ASN404E, ASN404F, ASN484F, ASP129E, ASP129F, ASP198E, ASP198F, ASP343E, ASP343F, CYS196E, CYS196F, CYS214F, CYS95E, CYS95F, GLN124E, GLN124F, GLN210E, GLN210F, GLN400E, GLN422F, GLN74E, GLN74F, GLN85E, GLN85F, GLU105E, GLU105F, GLU123E, GLU123F, GLU191E, GLU191F, GLU233E, GLU233F, GLU408E, GLU408F, GLU419E, GLU419F, GLY100E, GLY100F, GLY103E, GLY103F, GLY179E, GLY207E, GLY212F, GLY232E, GLY232F, GLY410E, GLY410F, GLY416E, GLY416F, GLY81E, GLY81F, GLY94E, GLY94F, GLY98E, GLY98F, HIS132E, HIS132F, HIS133E, HIS133F, HIS192E, HIS192F, HIS216F, HIS77E, HIS77F, HIS96E, HIS96F, ILE211E, ILE211F, ILE231E, ILE231F, ILE381F, ILE411F, LEU102E, LEU102F, LEU106E, LEU106F, LEU131E, LEU131F, LEU181E, LEU181F, LEU197E, LEU199E, LEU199F, LEU204F, LEU208E, LEU208F, LEU385F, LEU406F, LEU407E, LEU407F, LEU418E, LEU418F, LEU428F, LEU79E, LEU79F, LEU86E, LYS108E, LYS108F, LYS134E, LYS134F, LYS180E, LYS202E, LYS202F, LYS229E, LYS229F, LYS234E, LYS234F, LYS382E, LYS431F, LYS483F, MET421E, MET421F, MET435E, MET435F, PHE121E, PHE121F, PHE126E, PHE126F, PHE215E, PHE215F, PHE403E, PHE403F, PHE78F, PHE99E, PHE99F, PRO101E, PRO101F, PRO127E, PRO127F, PRO135E, PRO135F, PRO380F, PRO415E, PRO415F, PRO97E, PRO97F, SER117E, SER230E, SER230F, SER412E, SER412F, SER423E, SER423F, SER80E, SER80F, SER82E, SER82F, THR116E, THR116F, THR235E, THR235F, THR420E, THR420F, TRP115E, TRP115F, TRP414E, TRP414F, TYR206E, TYR417E, TYR417F, TYR432F, VAL104E, VAL104F, VAL118E, VAL119E, VAL119F, VAL120E, VAL120F, VAL125E, VAL125F, VAL128E, VAL128F, VAL194E, VAL194F, VAL200E, VAL200F, VAL213E, VAL213F, VAL383F, VAL413E, VAL413F