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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Molecule viewer


Only interaction residues
#binding
partners
  2
  1
  0

Sequence information

1   MGHHHHHHRK   VQMGAKDATP   VPCGRWAKIL   EKDKRTQQMR   MQRLKAKLQM   50
51   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)		 Disease name
229_PHE SER 8.3kJPN
chr19:629676 		-
- 0.0002 -
229_PHE VAL 8.3kJPN
chr19:629677 		-
- 0.0002 -
250_HIS ASP VAR_086919 rs137994680
LP/P - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
250_HIS ASP ClinVar
chr19:629614 		rs137994680
Pathogenic - Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
250_HIS ASP gnomAD
chr19:629614 		rs137994680
- 0.000195894 -
253_ARG TRP gnomAD
chr19:629605 		rs145312875
- 0.000496922 -
256_ARG GLN gnomAD
chr19:629595 		rs140683573
- 0.000452745 -
263_MET THR gnomAD
chr19:629574 		rs753398978
- 0.000132226 -
272_ALA VAL 8.3kJPN
chr19:629547 		rs1339218084
- 0.0001 -
273_ARG GLN 8.3kJPN
chr19:629544 		rs775562722
- 0.0001 -
294_PRO LEU gnomAD
chr19:625196 		rs566027653
- 0.00012341 -
316_ILE VAL gnomAD
chr19:625131 		rs115263594
- 0.000911288 -
318_ARG SER 8.3kJPN
chr19:624905 		-
- 0.0004 -
322_GLN LEU gnomAD
chr19:624894 		rs138732981
- 0.00996397 -
323_MET ILE gnomAD
chr19:624890 		rs143022703
- 0.00228873 -
327_GLY ARG 8.3kJPN
chr19:624880 		rs1332937945
- 0.0001 -
336_ALA THR gnomAD
chr19:624853 		rs564966591
- 0.00039563 -
337_VAL ILE 8.3kJPN
chr19:624850 		rs201346718
- 0.0001 -
346_THR ALA 8.3kJPN
chr19:624823 		rs777572472
- 0.0001 -
357_THR PRO 8.3kJPN
chr19:624790 		rs770914181
- 0.0002 -
361_PRO LEU gnomAD
chr19:624777 		rs141638617
- 0.000147726 -
362_PRO LEU 8.3kJPN
chr19:624774 		rs368177502
- 0.0001 -
362_PRO SER 8.3kJPN
chr19:624775 		-
- 0.0001 -
366_PRO SER gnomAD
chr19:624763 		rs201473800
- 0.000546653 -
366_PRO SER 8.3kJPN
chr19:624763 		rs201473800
- 0.0018 -
367_PRO LEU 8.3kJPN
chr19:624759 		rs374260495
- 0.0001 -
367_PRO ALA 8.3kJPN
chr19:624760 		rs146221322
- 0.0025 -
368_VAL ILE gnomAD
chr19:624757 		rs141630265
- 0.00027521 -
369_ASN SER 8.3kJPN
chr19:624753 		rs749862454
- 0.0002 -
400_PHE LEU gnomAD
chr19:623546 		rs41553913
- 0.0182972 -
417_VAL MET gnomAD
chr19:623495 		rs142443929
- 0.000239383 -
421_THR ARG 8.3kJPN
chr19:623482 		-
- 0.0001 -
429_HIS ARG gnomAD
chr19:623458 		rs147681201
- 0.000516235 -
438_ARG GLN 8.3kJPN
chr19:622963 		-
- 0.0002 -
441_TRP SER 8.3kJPN
chr19:622954 		-
- 0.0001 -
444_ALA VAL gnomAD
chr19:622945 		rs148655029
- 0.000185284 -
447_ARG GLN gnomAD
chr19:622936 		rs144179084
- 0.000362585 -
447_ARG GLN 8.3kJPN
chr19:622936 		rs144179084
- 0.0009 -
464_ARG TRP 8.3kJPN
chr19:622886 		rs775678643
- 0.0001 -
473_LEU VAL 8.3kJPN
chr19:622859 		-
- 0.0001 -
481_ARG PRO gnomAD
chr19:622834 		rs146178977
- 0.000660123 -
482_MET ILE gnomAD
chr19:622830 		rs138594532
- 0.000115381 -
482_MET VAL gnomAD
chr19:622832 		rs141490879
- 0.000675133 -
482_MET LEU 8.3kJPN
chr19:622832 		rs141490879
- - -
483_LEU PHE 8.3kJPN
chr19:622829 		rs760945130
- 0.0001 -
500_LEU PRO 8.3kJPN
chr19:622709 		-
- 0.0001 -
509_PHE LEU 8.3kJPN
chr19:622681 		-
- 0.0001 -
511_ARG GLN 8.3kJPN
chr19:622676 		rs1245111840
- 0.0001 -
526_LEU VAL 8.3kJPN
chr19:622632 		-
- 0.0002 -
534_LEU PHE 8.3kJPN
chr19:622608 		rs764456049
- 0.0002 -
539_SER PHE gnomAD
chr19:622592 		rs143834673
- 0.000145163 -
541_ALA SER gnomAD
chr19:622587 		rs56226067
- 0.000497573 -
541_ALA SER 8.3kJPN
chr19:622587 		rs56226067
- 0.011 -
545_GLU LYS gnomAD
chr19:622367 		rs115950441
- 0.000486084 -
550_ARG TRP 8.3kJPN
chr19:622352 		-
- 0.0001 -
551_GLN HIS gnomAD
chr19:622347 		rs202005794
- 0.000585587 -
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 -
566_PRO SER VAR_086920 rs41545023
LP/P - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
566_PRO SER gnomAD
chr19:622304 		rs41545023
- 0.00130765 -
611_SER PHE VAR_086921 -
LP/P - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
611_SER PHE ClinVar
chr19:622168 		rs2144625053
Pathogenic - 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 -
626_ALA THR 8.3kJPN
chr19:621822 		rs747554799
- 0.0005 -
641_PHE LEU VAR_086922 -
LP/P - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
641_PHE LEU ClinVar
chr19:621775 		rs748687181
Pathogenic - Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
643_ALA VAL gnomAD
chr19:621770 		rs775041868
- 0.000105331 -
656_THR LYS gnomAD
chr19:621731 		rs150982430
- 0.000123003 -
678_THR MET 8.3kJPN
chr19:621665 		rs1430315671
- 0.0001 -
681_GLN TER 8.3kJPN
chr19:621657 		rs776192083
- 0.0001 -
683_LEU VAL 8.3kJPN
chr19:621651 		rs770415736
- 0.0004 -
685_GLU GLY 8.3kJPN
chr19:621644 		-
- 0.0001 -
688_PRO SER 8.3kJPN
chr19:621636 		-
- 0.0002 -
691_ALA VAL 8.3kJPN
chr19:621626 		-
- 0.0001 -
698_ALA THR 8.3kJPN
chr19:621606 		-
- 0.0001 -
699_LEU VAL gnomAD
chr19:621603 		rs376907483
- 0.000356023 -
711_GLY GLU gnomAD
chr19:621566 		rs768516790
- 0.000281365 -
711_GLY ARG gnomAD
chr19:621567 		rs200645726
- 0.00030686 -
712_ARG LEU 8.3kJPN
chr19:621563 		rs547767015
- - -
713_VAL LEU gnomAD
chr19:621561 		rs10421235
- 0.0593861 -
713_VAL LEU 8.3kJPN
chr19:621561 		rs10421235
- 0.0862 -
717_VAL MET 8.3kJPN
chr19:621549 		rs1380944961
- 0.0004 -
723_ALA VAL 8.3kJPN
chr19:621530 		rs1363815639
- 0.0177 -
726_CYS TYR 8.3kJPN
chr19:621521 		rs562147939
- 0.0001 -
734_PRO LEU 8.3kJPN
chr19:621497 		rs1267559063
- 0.0001 -
734_PRO SER 8.3kJPN
chr19:621498 		-
- 0.0001 -
735_PRO LEU gnomAD
chr19:621494 		rs758721890
- 0.000183824 -
788_HIS ASP 8.3kJPN
chr19:621336 		-
- 0.0001 -
806_THR PRO 8.3kJPN
chr19:621282 		rs757781469
- 0.0002 -
807_TYR SER 8.3kJPN
chr19:621278 		-
- 0.0015 -
808_PRO SER 8.3kJPN
chr19:621276 		rs778477461
- 0.0002 -
810_PRO SER VAR_086924 -
US - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
810_PRO SER ClinVar
chr19:621270 		rs201364510
Pathogenic - Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
810_PRO SER gnomAD
chr19:621270 		rs201364510
- 0.0012648 -
822_ARG GLY 8.3kJPN
chr19:621234 		-
- 0.0001 -
840_TRP TER 8.3kJPN
chr19:621179 		-
- 0.0001 -
843_ILE VAL 8.3kJPN
chr19:621171 		rs751459962
- 0.0002 -
858_ARG TRP gnomAD
chr19:621126 		rs559084202
- 0.000252774 -
859_LYS MET 8.3kJPN
chr19:621122 		-
- 0.0001 -
864_ALA VAL 8.3kJPN
chr19:621107 		rs775039991
- 0.0001 -
870_ASP ASN VAR_086925 -
US - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
870_ASP ASN ClinVar
chr19:621090 		rs139383492
Pathogenic - Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
870_ASP ASN gnomAD
chr19:621090 		rs139383492
- 0.00322541 -
875_ALA VAL 8.3kJPN
chr19:621074 		rs767856533
- 0.0002 -
877_GLN ARG gnomAD
chr19:621068 		rs759041307
- 0.000112776 -
884_TRP SER 8.3kJPN
chr19:620477 		-
- 0.0001 -
898_CYS SER gnomAD
chr19:620435 		rs143868040
- 0.000102751 -
900_GLU LYS 8.3kJPN
chr19:620430 		rs796052172
- 0.0001 -
903_ASN LYS 8.3kJPN
chr19:620419 		-
- 0.0001 -
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 -
947_GLU LYS gnomAD
chr19:620005 		rs151235528
- 0.00187343 -
954_ASP GLU gnomAD
chr19:619982 		rs200607630
- 0.000103446 -
963_VAL MET 8.3kJPN
chr19:619765 		-
- 0.0001 -
994_VAL GLY 8.3kJPN
chr19:619671 		-
- 0.0002 -
1013_ARG CYS VAR_086927 -
LP/P - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
1013_ARG CYS ClinVar
chr19:619615 		rs745348188
Pathogenic - Combined oxidative phosphorylation deficiency 55 [MONDO:MONDO:0859228,MedGen:C5676915,OMIM:619743]
1014_LEU PHE 8.3kJPN
chr19:619612 		-
- 0.0001 -
1015_ARG TRP 8.3kJPN
chr19:619609 		rs751370183
- 0.0005 -
1034_ARG CYS 8.3kJPN
chr19:619263 		-
- 0.0045 -
1041_GLN LYS 8.3kJPN
chr19:619242 		-
- 0.0006 -
1045_SER LEU gnomAD
chr19:619229 		rs199504612
- 0.000135683 -
1059_ARG CYS 8.3kJPN
chr19:619089 		rs757765767
- 0.0001 -
1076_VAL ILE 8.3kJPN
chr19:619038 		rs746274300
- 0.0001 -
1078_VAL ILE 8.3kJPN
chr19:619032 		rs370808958
- 0.0001 -
1113_ARG GLY 8.3kJPN
chr19:618573 		rs751211087
- 0.0002 -
1117_ASN SER 8.3kJPN
chr19:618560 		-
- 0.0001 -
1120_PRO LEU 8.3kJPN
chr19:618551 		rs772321080
- 0.0002 -
1148_SER PHE 8.3kJPN
chr19:617829 		-
- 0.0001 -
1149_VAL MET 8.3kJPN
chr19:617827 		-
- 0.0001 -
1159_ASP ALA 8.3kJPN
chr19:617796 		-
- 0.0001 -
1173_ARG CYS gnomAD
chr19:617634 		rs147740567
- 0.000437235 -
1190_ARG GLN gnomAD
chr19:617582 		rs150648879
- 0.000168809 -
1193_SER PHE VAR_086928 rs142850300
LP/P - Combined oxidative phosphorylation deficiency 55 (COXPD55) [MIM:619743]
1193_SER PHE gnomAD
chr19:617573 		rs142850300
- 0.00122324 -
1198_ILE LEU gnomAD
chr19:617470 		rs138715064
- 0.000114987 -
1199_LEU SER gnomAD
chr19:617466 		rs151287767
- 0.0061553 -
1218_ASP HIS 8.3kJPN
chr19:617315 		rs563746524
- 0.0001 -
1220_GLU GLY 8.3kJPN
chr19:617308 		rs905785861
- 0.0001 -
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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

COPYRIGHTc2008-2019 Miho Higurashi, Takashi Ishida and Kengo Kinoshita. All rights reserved.