PiSITE

PDB ID	3SPA	CHAIN	A
Protein name	DNA-directed RNA polymerase, mitochondrial
Uniprot Accession	O00411
The number of similar proteins	5
The number of binding states	3
The number of binding partners	3

Coloring

Unicolor (beige)

The number of binding partners

Group

Binding state	Binding partners
	3SPA (CHAIN: A)
1	Monomeric state
2	Q96QE5
3	Q9H5Q4 Q00059

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Only interaction residues

#binding
partners

	2
	1
	0

Sequence information

MGHHHHHHRK

VQMGAKDATP

VPCGRWAKIL

EKDKRTQQMR

MQRLKAKLQM

PFQSGEFKAL

TRRLQVEPRL

LSKQMAGCLE

DCTRQAPESP

WEEQLARLLQ

100

101

EAPGKLSLDV

EQAPSGQHSQ

AQLSGQQQRL

LAFFKCCLLT

DQLPLAHHLL

150

151

VVHHGQRQKR

KLLTLDMYNA

VMLGWARQGA

FKELVYVLFM

VKDAGLTPDL

200

201

LSYAAALQCM

GRQDQDAGTI

ERCLEQMSQE

GLKLQALFTA

VLLSEEDRAT

250

251

VLKAVHKVKP

TFSLPPQLPP

PVNTSKLLRD

VYAKDGRVSY

PKLHLPLKTL

300

301

QCLFEKQLHM

ELASRVCVVS

VEKPTLPSKE

VKHARKTLKT

LRDQWEKALC

350

351

RALRETKNRL

EREVYEGRFS

LYPFLCLLDE

REVVRMLLQV

LQALPAQGES

400

401

FTTLARELSA

RTFSRHVVQR

QRVSGQVQAL

QNHYRKYLCL

LASDAEVPEP

450

451

CLPRQYWEAL

GAPEALREQP

WPLPVQMELG

KLLAEMLVQA

TQMPCSLDKP

500

501

HRSSRLVPVL

YHVYSFRNVQ

QIGILKPHPA

YVQLLEKAAE

PTLTFEAVDV

550

551

PMLCPPLPWT

SPHSGAFLLS

PTKLMRTVEG

ATQHQELLET

CPPTALHGAL

600

601

DALTQLGNCA

WRVNGRVLDL

VLQLFQAKGC

PQLGVPAPPS

EAPQPPEAHL

650

651

PHSAAPARKA

ELRRELAHCQ

KVAREMHSLR

AEALYRLSLA

QHLRDRVFWL

700

701

PHNMDFRGRT

YPCPPHFNHL

GSDVARALLE

FAQGRPLGPH

GLDWLKIHLV

750

751

NLTGLKKREP

LRKRLAFAEE

VMDDILDSAD

QPLTGRKWWM

GAEEPWQTLA

800

801

CCMEVANAVR

ASDPAAYVSH

LPVHQDGSCN

GLQHYAALGR

DSVGAASVNL

850

851

EPSDVPQDVY

SGVAAQVEVF

RRQDAQRGMR

VAQVLEGFIT

RKVVKQTVMT

900

901

VVYGVTRYGG

RLQIEKRLRE

LSDFPQEFVW

EASHYLVRQV

FKSLQEMFSG

950

951

TRAIQHWLTE

SARLISHMGS

VVEWVTPLGV

PVIQPYRLDS

KVKQIGGGIQ

1000

1001

SITYTHNGDI

SRKPNTRKQK

NGFPPNFIHS

LDSSHMMLTA

LHCYRKGLTF

1050

1051

VSVHDCYWTH

AADVSVMNQV

CREQFVRLHS

EPILQDLSRF

LVKRFCSEPQ

1100

1101

KILEASQLKE

TLQAVPKPGA

FDLEQVKRST

YFFS

1150

Variants

Residue	AA	Source / dbSNP	Clinical Significance	Allele Frequency (> 0.0001)	AlphaMissense pathogenicity	Disease name
229_PHE	SER	8.3kJPN chr19:629676 -	-	0.0002	0.8644	-
229_PHE	VAL	8.3kJPN chr19:629677 -	-	0.0002	0.5726	-
250_HIS	ASP	VAR_086919 rs137994680	LP/P	-	0.8813	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
250_HIS	ASP	ClinVar chr19:629614 rs137994680	Pathogenic	-	0.8813	Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
250_HIS	ASP	gnomAD chr19:629614 rs137994680	-	0.000195894	0.8813	-
253_ARG	TRP	gnomAD chr19:629605 rs145312875	-	0.000496922	0.0955	-
256_ARG	GLN	gnomAD chr19:629595 rs140683573	-	0.000452745	0.0627	-
263_MET	THR	gnomAD chr19:629574 rs753398978	-	0.000132226	0.5166	-
272_ALA	VAL	8.3kJPN chr19:629547 rs1339218084	-	0.0001	0.829	-
273_ARG	GLN	8.3kJPN chr19:629544 rs775562722	-	0.0001	0.0949	-
294_PRO	LEU	gnomAD chr19:625196 rs566027653	-	0.00012341	0.354	-
316_ILE	VAL	gnomAD chr19:625131 rs115263594	-	0.000911288	0.0996	-
318_ARG	SER	8.3kJPN chr19:624905 -	-	0.0004	0.5404	-
322_GLN	LEU	gnomAD chr19:624894 rs138732981	-	0.00996397	0.2607	-
323_MET	ILE	gnomAD chr19:624890 rs143022703	-	0.00228873	0.7716	-
327_GLY	ARG	8.3kJPN chr19:624880 rs1332937945	-	0.0001	0.3198	-
336_ALA	THR	gnomAD chr19:624853 rs564966591	-	0.00039563	0.0737	-
337_VAL	ILE	8.3kJPN chr19:624850 rs201346718	-	0.0001	0.1064	-
346_THR	ALA	8.3kJPN chr19:624823 rs777572472	-	0.0001	0.0519	-
357_THR	PRO	8.3kJPN chr19:624790 rs770914181	-	0.0002	0.0959	-
361_PRO	LEU	gnomAD chr19:624777 rs141638617	-	0.000147726	0.0991	-
362_PRO	LEU	8.3kJPN chr19:624774 rs368177502	-	0.0001	0.0834	-
362_PRO	SER	8.3kJPN chr19:624775 -	-	0.0001	0.0878	-
366_PRO	SER	gnomAD chr19:624763 rs201473800	-	0.000546653	0.0773	-
366_PRO	SER	8.3kJPN chr19:624763 rs201473800	-	0.0018	0.0773	-
367_PRO	LEU	8.3kJPN chr19:624759 rs374260495	-	0.0001	0.0781	-
367_PRO	ALA	8.3kJPN chr19:624760 rs146221322	-	0.0025	0.0514	-
368_VAL	ILE	gnomAD chr19:624757 rs141630265	-	0.00027521	0.0893	-
369_ASN	SER	8.3kJPN chr19:624753 rs749862454	-	0.0002	0.1039	-
400_PHE	LEU	gnomAD chr19:623546 rs41553913	-	0.0182972	0.8839	-
417_VAL	MET	gnomAD chr19:623495 rs142443929	-	0.000239383	0.303	-
421_THR	ARG	8.3kJPN chr19:623482 -	-	0.0001	0.0851	-
429_HIS	ARG	gnomAD chr19:623458 rs147681201	-	0.000516235	0.0658	-
438_ARG	GLN	8.3kJPN chr19:622963 -	-	0.0002	0.082	-
441_TRP	SER	8.3kJPN chr19:622954 -	-	0.0001	0.8797	-
444_ALA	VAL	gnomAD chr19:622945 rs148655029	-	0.000185284	0.1129	-
447_ARG	GLN	gnomAD chr19:622936 rs144179084	-	0.000362585	0.0747	-
447_ARG	GLN	8.3kJPN chr19:622936 rs144179084	-	0.0009	0.0747	-
464_ARG	TRP	8.3kJPN chr19:622886 rs775678643	-	0.0001	0.1409	-
473_LEU	VAL	8.3kJPN chr19:622859 -	-	0.0001	0.0942	-
481_ARG	PRO	gnomAD chr19:622834 rs146178977	-	0.000660123	0.371	-
482_MET	ILE	gnomAD chr19:622830 rs138594532	-	0.000115381	0.4101	-
482_MET	VAL	gnomAD chr19:622832 rs141490879	-	0.000675133	0.1759	-
482_MET	LEU	8.3kJPN chr19:622832 rs141490879	-	-	0.1312	-
483_LEU	PHE	8.3kJPN chr19:622829 rs760945130	-	0.0001	0.3584	-
500_LEU	PRO	8.3kJPN chr19:622709 -	-	0.0001	0.809	-
509_PHE	LEU	8.3kJPN chr19:622681 -	-	0.0001	0.8708	-
511_ARG	GLN	8.3kJPN chr19:622676 rs1245111840	-	0.0001	0.095	-
526_LEU	VAL	8.3kJPN chr19:622632 -	-	0.0002	0.1208	-
534_LEU	PHE	8.3kJPN chr19:622608 rs764456049	-	0.0002	0.483	-
539_SER	PHE	gnomAD chr19:622592 rs143834673	-	0.000145163	0.2124	-
541_ALA	SER	gnomAD chr19:622587 rs56226067	-	0.000497573	0.0758	-
541_ALA	SER	8.3kJPN chr19:622587 rs56226067	-	0.011	0.0758	-
545_GLU	LYS	gnomAD chr19:622367 rs115950441	-	0.000486084	0.0689	-
550_ARG	TRP	8.3kJPN chr19:622352 -	-	0.0001	0.6386	-
551_GLN	HIS	gnomAD chr19:622347 rs202005794	-	0.000585587	0.427	-
555_GLU	ALA	gnomAD chr19:622336 rs2238549	-	0.508629	-	-
555_GLU	ALA	8.3kJPN chr19:622336 rs2238549	-	0.5496	-	-
558_ALA	THR	8.3kJPN chr19:622328 rs755299102	-	0.0004	0.0696	-
566_PRO	SER	VAR_086920 rs41545023	LP/P	-	0.1504	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
566_PRO	SER	gnomAD chr19:622304 rs41545023	-	0.00130765	0.1504	-
611_SER	PHE	VAR_086921 -	LP/P	-	0.5635	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
611_SER	PHE	ClinVar chr19:622168 rs2144625053	Pathogenic	-	0.5635	Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
616_GLN	TER	8.3kJPN chr19:622154 rs768967483	-	0.0001	-	-
623_PRO	LEU	gnomAD chr19:621830 rs370122679	-	0.000153284	0.3783	-
626_ALA	THR	8.3kJPN chr19:621822 rs747554799	-	0.0005	0.1039	-
641_PHE	LEU	VAR_086922 -	LP/P	-	0.9531	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
641_PHE	LEU	ClinVar chr19:621775 rs748687181	Pathogenic	-	0.9531	Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
643_ALA	VAL	gnomAD chr19:621770 rs775041868	-	0.000105331	0.1332	-
656_THR	LYS	gnomAD chr19:621731 rs150982430	-	0.000123003	0.1728	-
678_THR	MET	8.3kJPN chr19:621665 rs1430315671	-	0.0001	0.0663	-
681_GLN	TER	8.3kJPN chr19:621657 rs776192083	-	0.0001	-	-
683_LEU	VAL	8.3kJPN chr19:621651 rs770415736	-	0.0004	0.12	-
685_GLU	GLY	8.3kJPN chr19:621644 -	-	0.0001	0.1549	-
688_PRO	SER	8.3kJPN chr19:621636 -	-	0.0002	0.0837	-
691_ALA	VAL	8.3kJPN chr19:621626 -	-	0.0001	0.0898	-
698_ALA	THR	8.3kJPN chr19:621606 -	-	0.0001	0.0775	-
699_LEU	VAL	gnomAD chr19:621603 rs376907483	-	0.000356023	0.1324	-
711_GLY	GLU	gnomAD chr19:621566 rs768516790	-	0.000281365	0.1851	-
711_GLY	ARG	gnomAD chr19:621567 rs200645726	-	0.00030686	0.1432	-
712_ARG	LEU	8.3kJPN chr19:621563 rs547767015	-	-	0.1743	-
713_VAL	LEU	gnomAD chr19:621561 rs10421235	-	0.0593861	0.12	-
713_VAL	LEU	8.3kJPN chr19:621561 rs10421235	-	0.0862	0.12	-
717_VAL	MET	8.3kJPN chr19:621549 rs1380944961	-	0.0004	0.2749	-
723_ALA	VAL	8.3kJPN chr19:621530 rs1363815639	-	0.0177	0.1345	-
726_CYS	TYR	8.3kJPN chr19:621521 rs562147939	-	0.0001	0.2247	-
734_PRO	LEU	8.3kJPN chr19:621497 rs1267559063	-	0.0001	0.0955	-
734_PRO	SER	8.3kJPN chr19:621498 -	-	0.0001	0.0808	-
735_PRO	LEU	gnomAD chr19:621494 rs758721890	-	0.000183824	0.0994	-
788_HIS	ASP	8.3kJPN chr19:621336 -	-	0.0001	0.5298	-
806_THR	PRO	8.3kJPN chr19:621282 rs757781469	-	0.0002	0.5876	-
807_TYR	SER	8.3kJPN chr19:621278 -	-	0.0015	0.9391	-
808_PRO	SER	8.3kJPN chr19:621276 rs778477461	-	0.0002	0.7422	-
810_PRO	SER	VAR_086924 -	US	-	0.1933	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
810_PRO	SER	ClinVar chr19:621270 rs201364510	Pathogenic	-	0.1933	Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
810_PRO	SER	gnomAD chr19:621270 rs201364510	-	0.0012648	0.1933	-
822_ARG	GLY	8.3kJPN chr19:621234 -	-	0.0001	0.9538	-
840_TRP	TER	8.3kJPN chr19:621179 -	-	0.0001	-	-
843_ILE	VAL	8.3kJPN chr19:621171 rs751459962	-	0.0002	0.1533	-
858_ARG	TRP	gnomAD chr19:621126 rs559084202	-	0.000252774	0.0848	-
859_LYS	MET	8.3kJPN chr19:621122 -	-	0.0001	0.1086	-
864_ALA	VAL	8.3kJPN chr19:621107 rs775039991	-	0.0001	0.2286	-
870_ASP	ASN	VAR_086925 -	US	-	0.1058	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
870_ASP	ASN	ClinVar chr19:621090 rs139383492	Pathogenic	-	0.1058	Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
870_ASP	ASN	gnomAD chr19:621090 rs139383492	-	0.00322541	0.1058	-
875_ALA	VAL	8.3kJPN chr19:621074 rs767856533	-	0.0002	0.4386	-
877_GLN	ARG	gnomAD chr19:621068 rs759041307	-	0.000112776	0.0513	-
884_TRP	SER	8.3kJPN chr19:620477 -	-	0.0001	0.9253	-
898_CYS	SER	gnomAD chr19:620435 rs143868040	-	0.000102751	0.5318	-
900_GLU	LYS	8.3kJPN chr19:620430 rs796052172	-	0.0001	0.9246	-
903_ASN	LYS	8.3kJPN chr19:620419 -	-	0.0001	0.0834	-
925_CYS	TER	ClinVar chr19:620069 rs55752843	Pathogenic	-	-	Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
941_ALA	THR	8.3kJPN chr19:620023 -	-	0.0001	0.8954	-
947_GLU	LYS	gnomAD chr19:620005 rs151235528	-	0.00187343	0.0778	-
954_ASP	GLU	gnomAD chr19:619982 rs200607630	-	0.000103446	0.9862	-
963_VAL	MET	8.3kJPN chr19:619765 -	-	0.0001	0.6982	-
994_VAL	GLY	8.3kJPN chr19:619671 -	-	0.0002	0.9699	-
1013_ARG	CYS	VAR_086927 -	LP/P	-	0.2265	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
1013_ARG	CYS	ClinVar chr19:619615 rs745348188	Pathogenic	-	0.2265	Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
1014_LEU	PHE	8.3kJPN chr19:619612 -	-	0.0001	0.7525	-
1015_ARG	TRP	8.3kJPN chr19:619609 rs751370183	-	0.0005	0.1304	-
1034_ARG	CYS	8.3kJPN chr19:619263 -	-	0.0045	0.0855	-
1041_GLN	LYS	8.3kJPN chr19:619242 -	-	0.0006	0.1312	-
1045_SER	LEU	gnomAD chr19:619229 rs199504612	-	0.000135683	0.0964	-
1059_ARG	CYS	8.3kJPN chr19:619089 rs757765767	-	0.0001	0.1442	-
1076_VAL	ILE	8.3kJPN chr19:619038 rs746274300	-	0.0001	0.0482	-
1078_VAL	ILE	8.3kJPN chr19:619032 rs370808958	-	0.0001	0.0719	-
1113_ARG	GLY	8.3kJPN chr19:618573 rs751211087	-	0.0002	0.3522	-
1117_ASN	SER	8.3kJPN chr19:618560 -	-	0.0001	0.4663	-
1120_PRO	LEU	8.3kJPN chr19:618551 rs772321080	-	0.0002	0.8351	-
1148_SER	PHE	8.3kJPN chr19:617829 -	-	0.0001	0.9943	-
1149_VAL	MET	8.3kJPN chr19:617827 -	-	0.0001	0.888	-
1159_ASP	ALA	8.3kJPN chr19:617796 -	-	0.0001	0.4655	-
1173_ARG	CYS	gnomAD chr19:617634 rs147740567	-	0.000437235	0.0872	-
1190_ARG	GLN	gnomAD chr19:617582 rs150648879	-	0.000168809	0.1161	-
1193_SER	PHE	VAR_086928 rs142850300	LP/P	-	0.1389	Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
1193_SER	PHE	gnomAD chr19:617573 rs142850300	-	0.00122324	0.1389	-
1198_ILE	LEU	gnomAD chr19:617470 rs138715064	-	0.000114987	0.0673	-
1199_LEU	SER	gnomAD chr19:617466 rs151287767	-	0.0061553	0.0843	-
1218_ASP	HIS	8.3kJPN chr19:617315 rs563746524	-	0.0001	0.1529	-
1220_GLU	GLY	8.3kJPN chr19:617308 rs905785861	-	0.0001	0.0963	-

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Reference

PiSite: a database of protein interaction sites using multiple binding states in the PDB, Miho Higurashi, Takashi Ishida and Kengo Kinoshita, Nucleic Acids Research 2009 37(Database issue):D360-D364

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Sequence information

Binding partner information

Binding partner information

Binding partner information

Variants

Reference

	Q9H5Q4	Dimethyladenosine transferase 2, mitochondrial
	Q00059	Transcription factor A, mitochondrial