PiSITE

PDB ID	2PMW	CHAIN	B
Protein name	Proprotein convertase subtilisin/kexin type 9
Uniprot Accession	Q5SZQ2
The number of similar proteins	16
The number of binding states	5
The number of binding partners	5

Coloring

Unicolor (beige)

The number of binding partners

Group

Binding state	Binding partners
	2PMW (CHAIN: B)
1	Q8NBP7
2	Q8NBP7 Q59FQ1
3	Q8NBP7 P01130
4	Q8NBP7 3SQO 3SQO
5	Q8NBP7 5VL7 5VL7

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Only interaction residues

#binding
partners

	5
	4
	3
	2
	1
	0

Sequence information

SIPWNLERIT

PPRYRADEYQ

PPDGGSLVEV

YLLDTSIQSD

HREIEGRVMV

TDFENVPEED

GTRFHRQASK

CDSHGTHLAG

VVSGRDAGVA

KGASMRSLRV

100

101

LNCQGKGTVS

GTLIGLEFIR

KSQLVQPVGP

LVVLLPLAGG

YSRVLNAACQ

150

151

RLARAGVVLV

TAAGNFRDDA

CLYSPASAPE

VITVGATNAQ

DQPVTLGTLG

200

201

TNFGRCVDLF

APGEDIIGAS

SDCSTCFVSQ

SGTSQAAAHV

AGIAAMMLSA

250

251

EPELTLAELR

QRLIHFSAKD

VINEAWFPED

QRVLTPNLVA

ALPPSTHGAG

300

301

WQLFCRTVWS

AHSGPTRMAT

AVARCAPDEE

LLSCSSFSRS

GKRRGERMEA

350

351

QGGKLVCRAH

NAFGGEGVYA

IARCCLLPQA

NCSVHTAPPA

EASMGTRVHC

400

401

HQQGHVLTGC

SSHWEVEDLG

THKPPVLRPR

GQPNQCVGHR

EASIHASCCH

450

451

APGLECKVKE

HGIPAPQEQV

TVACEEGWTL

TGCSALPGTS

HVLGAYAVDN

500

501

TCVVRSRDVS

TTGSTSEGAV

TAVAICCRSR

HLAQASQELQ

550

Variants

Residue	AA	Source / dbSNP	Clinical Significance	Allele Frequency (> 0.0001)	AlphaMissense pathogenicity	Disease name
153_SER	ASN	8.3kJPN chr1:55512254 -	-	0.0001	-	-
209_PRO	LEU	8.3kJPN chr1:55518053 -	-	0.0001	-	-
219_GLN	GLU	8.3kJPN chr1:55518082 rs778617372	-	0.0001	-	-
233_VAL	ALA	8.3kJPN chr1:55518363 -	-	0.0001	-	-
236_GLY	SER	8.3kJPN chr1:55518371 rs149489325	-	0.0001	-	-
237_ARG	TRP	gnomAD chr1:55518374 rs148195424	-	0.000718598	-	-
237_ARG	TRP	8.3kJPN chr1:55518374 rs148195424	-	0.0001	-	-
241_VAL	MET	8.3kJPN chr1:55518386 rs147478188	-	0.0001	-	-
246_SER	ASN	8.3kJPN chr1:55518402 -	-	0.0001	-	-
248_ARG	CYS	8.3kJPN chr1:55518407 rs779824389	-	0.0002	-	-
253_LEU	PHE	gnomAD chr1:55518422 rs72646508	-	0.000192791	-	-
263_GLY	SER	8.3kJPN chr1:55518452 rs200146448	-	0.007	-	-
264_THR	ILE	8.3kJPN chr1:55518456 rs201789841	-	0.0051	-	-
279_PRO	THR	gnomAD chr1:55521701 rs72646509	-	0.000308363	-	-
298_ASN	ASP	gnomAD chr1:55521758 rs575003139	-	0.000108556	-	-
310_VAL	MET	8.3kJPN chr1:55521794 rs1200999906	-	0.0001	-	-
323_CYS	SER	8.3kJPN chr1:55521834 rs1307302473	-	0.0001	-	-
354_ASN	ILE	ClinVar chr1:55523068 rs1553137543	Likely pathogenic	-	-	Hypercholesterolemia, familial, 1 [MONDO:MONDO:0007750,MedGen:C0745103,OMIM:143890,Orphanet:391665]
357_ARG	CYS	gnomAD chr1:55523076 rs148562777	-	0.00015117	-	-
357_ARG	CYS	8.3kJPN chr1:55523076 rs148562777	-	0.0001	-	-
367_ASP	HIS	gnomAD chr1:55523106 rs141867978	-	0.000230776	-	-
374_ASP	TYR	ClinVar chr1:55523127 rs137852912	Pathogenic/Likely pathogenic	-	-	Hypercholesterolemia, autosomal dominant, 3\|Hypercholesterolemia, familial, 1 [MONDO:MONDO:0011369,MedGen:C1863551,OMIM:603776\|MONDO:MONDO:0007750,MedGen:C0745103,OMIM:143890,Orphanet:391665]
374_ASP	HIS	ClinVar chr1:55523127 rs137852912	Pathogenic	-	-	Hypercholesterolemia, familial, 1\|Hypercholesterolemia, autosomal dominant, 3 [MONDO:MONDO:0007750,MedGen:C0745103,OMIM:143890,Orphanet:391665\|MONDO:MONDO:0011369,MedGen:C1863551,OMIM:603776]
378_CYS	TRP	8.3kJPN chr1:55523141 rs776752113	-	0.0001	-	-
391_HIS	ASN	gnomAD chr1:55523178 rs146471967	-	0.000162615	-	-
392_VAL	MET	ClinVar chr1:55523181 rs1254346075	Pathogenic	-	-	Hypercholesterolemia, familial, 1 [MONDO:MONDO:0007750,MedGen:C0745103,OMIM:143890,Orphanet:391665]
412_ARG	LYS	8.3kJPN chr1:55523763 rs775522541	-	0.0001	-	-
417_HIS	GLN	gnomAD chr1:55523779 rs143275858	-	0.000214927	-	-
424_ILE	VAL	8.3kJPN chr1:55523798 rs759250273	-	0.0092	-	-
425_ASN	SER	gnomAD chr1:55523802 rs28362261	-	0.00122609	-	-
428_TRP	TER	8.3kJPN chr1:55523812 -	-	0.0007	-	-
443_ALA	THR	gnomAD chr1:55523855 rs28362263	-	0.00719433	-	-
465_SER	TRP	ClinVar chr1:55524211 -	Likely pathogenic	-	-	Hypercholesterolemia, autosomal dominant, 3 [MONDO:MONDO:0011369,MedGen:C1863551,OMIM:603776]
467_PRO	LEU	8.3kJPN chr1:55524217 -	-	0.0001	-	-
468_THR	ALA	ClinVar chr1:55524219 rs1553137693	Pathogenic	-	-	Hypercholesterolemia, familial, 1 [MONDO:MONDO:0007750,MedGen:C0745103,OMIM:143890,Orphanet:391665]
469_ARG	TRP	gnomAD chr1:55524222 rs141502002	-	0.00060473	-	-
471_ALA	SER	ClinVar chr1:55524228 rs1553137699	Pathogenic	-	-	Hypercholesterolemia, familial, 1 [MONDO:MONDO:0007750,MedGen:C0745103,OMIM:143890,Orphanet:391665]
474_VAL	ILE	gnomAD chr1:55524237 rs562556	-	0.856674	-	-
474_VAL	ILE	8.3kJPN chr1:55524237 rs562556	-	0.9687	-	-
495_ARG	TRP	8.3kJPN chr1:55524300 rs758999339	-	0.0001	-	-
496_ARG	GLN	gnomAD chr1:55524304 rs139669564	-	0.000254051	-	-
499_ARG	CYS	gnomAD chr1:55524312 rs201395805	-	0.000126901	-	-
499_ARG	CYS	8.3kJPN chr1:55524312 rs201395805	-	0.0002	-	-
504_GLY	TRP	8.3kJPN chr1:55525165 rs374455190	-	0.0001	-	-
510_ARG	TRP	8.3kJPN chr1:55525183 rs751649334	-	0.0001	-	-
514_ALA	THR	8.3kJPN chr1:55525195 rs1447116791	-	0.0001	-	-
522_ALA	THR	8.3kJPN chr1:55525219 rs777300852	-	0.0001	-	-
536_VAL	ILE	gnomAD chr1:55525261 rs776367625	-	0.000138509	-	-
549_ARG	PRO	8.3kJPN chr1:55525301 -	-	0.0001	-	-
553_HIS	ARG	gnomAD chr1:55525313 rs28362270	-	0.000732503	-	-
554_GLN	GLU	gnomAD chr1:55525315 rs149311926	-	0.00017853	-	-
589_VAL	MET	8.3kJPN chr1:55527131 rs372586224	-	0.0002	-	-
591_HIS	GLN	gnomAD chr1:55527139 rs529912877	-	0.000140526	-	-
592_ARG	THR	8.3kJPN chr1:55527141 -	-	0.0001	-	-
598_ALA	THR	gnomAD chr1:55527158 rs367606156	-	0.000103727	-	-
598_ALA	THR	8.3kJPN chr1:55527158 rs367606156	-	0.0002	-	-
616_PRO	LEU	8.3kJPN chr1:55527213 rs755750316	-	0.0001	-	-
619_GLN	PRO	gnomAD chr1:55527222 rs28362277	-	0.00096086	-	-
629_GLY	ASP	8.3kJPN chr1:55529064 rs1261496250	-	0.0007	-	-
636_SER	ARG	ClinVar chr1:55529084 rs2100343401	Likely pathogenic	-	-	Hypercholesterolemia, autosomal dominant, 3 [MONDO:MONDO:0011369,MedGen:C1863551,OMIM:603776]
644_VAL	ILE	8.3kJPN chr1:55529108 rs143291739	-	0.0035	-	-
659_ARG	GLY	8.3kJPN chr1:55529153 rs147182054	-	0.0001	-	-
670_GLY	GLU	gnomAD chr1:55529187 rs505151	-	0.947698	-	-
670_GLY	GLU	8.3kJPN chr1:55529187 rs505151	-	0.9528	-	-
675_VAL	ILE	8.3kJPN chr1:55529201 rs760981278	-	0.0001	-	-
680_ARG	TRP	gnomAD chr1:55529216 rs533555352	-	0.000310126	-	-
680_ARG	LEU	8.3kJPN chr1:55529217 -	-	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

Coloring

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Sequence information

Binding partner information

Binding partner information

Binding partner information

Binding partner information

Binding partner information

Variants

Reference

	Q8NBP7	Proprotein convertase subtilisin/kexin type 9
	Q59FQ1	Low density lipoprotein receptor variant

	Q8NBP7	Proprotein convertase subtilisin/kexin type 9
	P01130	Low-density lipoprotein receptor

	Q8NBP7	Proprotein convertase subtilisin/kexin type 9
	5VL7	Fab33 light chain
	5VL7	Fab33 heavy chain

	Q8NBP7	PCSK9 prodomain
	3SQO	J16 Light chain
	3SQO	J16 Heavy chain