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3GCX
Asym. Unit
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Asym.Unit (93 KB)
Biol.Unit 1 (87 KB)
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(1)
Title
:
PCSK9:EGFA (PH 7.4)
Authors
:
M. C. Mcnutt, H. J. Kwon, C. Chen, J. R. Chen, J. D. Horton, T. A. Lagace
Date
:
22 Feb 09 (Deposition) - 03 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,E,P
Biol. Unit 1: A,E,P (1x)
Keywords
:
Pcsk9, Ldl Receptor, Autocatalytic Cleavage, Cholesterol Metabolism, Disease Mutation, Glycoprotein, Hydrolase, Lipid Metabolism, Phosphoprotein, Protease, Secreted, Serine Protease, Steroid Metabolism, Zymogen, Coated Pit, Egf-Like Domain, Endocytosis, Host- Virus Interaction, Ldl, Lipid Transport, Membrane, Receptor, Transmembrane, Transport, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Mcnutt, H. J. Kwon, C. Chen, J. R. Chen, J. D. Horton, T. A. Lagace
Antagonism Of Secreted Pcsk9 Increases Low Density Lipoprotein Receptor Expression In Hepg2 Cells.
J. Biol. Chem. V. 284 10561 2009
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET E:292 , THR E:294 , GLU E:296 , ASP E:310 , LEU E:311 , GLY E:314
BINDING SITE FOR RESIDUE CA E 1
[
close Site info
]
SAPs(SNPs)/Variants
(44, 44)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_058520 (T77I, chain P, )
02: VAR_058521 (R93C, chain P, )
03: VAR_058522 (G106R, chain P, )
04: VAR_058523 (V114A, chain P, )
05: VAR_017199 (S127R, chain P, )
06: VAR_058524 (D129G, chain P, )
07: VAR_058525 (N157K, chain A, )
08: VAR_025452 (R237W, chain A, )
09: VAR_058529 (A239D, chain A, )
10: VAR_025453 (L253F, chain A, )
11: VAR_005358 (M292Y, chain E, )
12: VAR_072841 (G293R, chain E, )
13: VAR_005360 (C297F, chain E, )
14: VAR_062376 (C297R, chain E, )
15: VAR_005359 (C297Y, chain E, )
16: VAR_072842 (S305C, chain E, )
17: VAR_005361 (H306Y, chain E, )
18: VAR_067196 (C308F, chain E, )
19: VAR_005362 (C308Y, chain E, )
20: VAR_005363 (G314S, chain E, )
21: VAR_005364 (C317S, chain E, )
22: VAR_005365 (D321E, chain E, )
23: VAR_005366 (D321N, chain E, )
24: VAR_005367 (G322S, chain E, )
25: VAR_005368 (R329P, chain E, )
26: VAR_072843 (C331R, chain E, )
27: VAR_005369 (C331Y, chain E, )
28: VAR_058530 (R357H, chain A, )
29: VAR_058531 (D374H, chain A, )
30: VAR_058532 (D374Y, chain A, )
31: VAR_025454 (H391N, chain A, )
32: VAR_067282 (G394S, chain A, )
33: VAR_025455 (H417Q, chain A, )
34: VAR_021337 (N425S, chain A, )
35: VAR_021338 (A443T, chain A, )
36: VAR_025456 (R469W, chain A, )
37: VAR_021339 (I474I, chain A, )
38: VAR_025457 (E482G, chain A, )
39: VAR_073657 (E482Q, chain A, )
40: VAR_058534 (R496W, chain A, )
41: VAR_025458 (F515L, chain A, )
42: VAR_058535 (A522T, chain A, )
43: VAR_058536 (P616L, chain A, )
44: VAR_021341 (Q619P, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_058520
T
77
I
PCSK9_HUMAN
Polymorphism
---
P
T
77
I
02
UniProt
VAR_058521
R
93
C
PCSK9_HUMAN
Polymorphism
151193009
P
R
93
C
03
UniProt
VAR_058522
G
106
R
PCSK9_HUMAN
Polymorphism
---
P
G
106
R
04
UniProt
VAR_058523
V
114
A
PCSK9_HUMAN
Polymorphism
---
P
V
114
A
05
UniProt
VAR_017199
S
127
R
PCSK9_HUMAN
Disease (HCHOLA3)
28942111
P
S
127
R
06
UniProt
VAR_058524
D
129
G
PCSK9_HUMAN
Disease (HCHOLA3)
---
P
D
129
G
07
UniProt
VAR_058525
N
157
K
PCSK9_HUMAN
Polymorphism
---
A
N
157
K
08
UniProt
VAR_025452
R
237
W
PCSK9_HUMAN
Polymorphism
---
A
R
237
W
09
UniProt
VAR_058529
A
239
D
PCSK9_HUMAN
Polymorphism
---
A
A
239
D
10
UniProt
VAR_025453
L
253
F
PCSK9_HUMAN
Polymorphism
28362270
A
L
253
F
11
UniProt
VAR_005358
C
313
Y
LDLR_HUMAN
Disease (FH)
---
E
M
292
Y
12
UniProt
VAR_072841
G
314
R
LDLR_HUMAN
Unclassified
---
E
G
293
R
13
UniProt
VAR_005360
C
318
F
LDLR_HUMAN
Disease (FH)
---
E
C
297
F
14
UniProt
VAR_062376
C
318
R
LDLR_HUMAN
Disease (FH)
---
E
C
297
R
15
UniProt
VAR_005359
C
318
Y
LDLR_HUMAN
Unclassified
---
E
C
297
Y
16
UniProt
VAR_072842
S
326
C
LDLR_HUMAN
Unclassified
---
E
S
305
C
17
UniProt
VAR_005361
H
327
Y
LDLR_HUMAN
Disease (FH)
---
E
H
306
Y
18
UniProt
VAR_067196
C
329
F
LDLR_HUMAN
Disease (FH)
---
E
C
308
F
19
UniProt
VAR_005362
C
329
Y
LDLR_HUMAN
Disease (FH)
---
E
C
308
Y
20
UniProt
VAR_005363
G
335
S
LDLR_HUMAN
Unclassified
---
E
G
314
S
21
UniProt
VAR_005364
C
338
S
LDLR_HUMAN
Disease (FH)
---
E
C
317
S
22
UniProt
VAR_005365
D
342
E
LDLR_HUMAN
Unclassified
---
E
D
321
E
23
UniProt
VAR_005366
D
342
N
LDLR_HUMAN
Unclassified
139361635
E
D
321
N
24
UniProt
VAR_005367
G
343
S
LDLR_HUMAN
Unclassified
---
E
G
322
S
25
UniProt
VAR_005368
R
350
P
LDLR_HUMAN
Disease (FH)
---
E
R
329
P
26
UniProt
VAR_072843
C
352
R
LDLR_HUMAN
Unclassified
---
E
C
331
R
27
UniProt
VAR_005369
C
352
Y
LDLR_HUMAN
Unclassified
---
E
C
331
Y
28
UniProt
VAR_058530
R
357
H
PCSK9_HUMAN
Disease (HCHOLA3)
---
A
R
357
H
29
UniProt
VAR_058531
D
374
H
PCSK9_HUMAN
Disease (HCHOLA3)
---
A
D
374
H
30
UniProt
VAR_058532
D
374
Y
PCSK9_HUMAN
Disease (HCHOLA3)
---
A
D
374
Y
31
UniProt
VAR_025454
H
391
N
PCSK9_HUMAN
Polymorphism
---
A
H
391
N
32
UniProt
VAR_067282
G
394
S
PCSK9_HUMAN
Unclassified
---
A
G
394
S
33
UniProt
VAR_025455
H
417
Q
PCSK9_HUMAN
Polymorphism
143275858
A
H
417
Q
34
UniProt
VAR_021337
N
425
S
PCSK9_HUMAN
Polymorphism
28362261
A
N
425
S
35
UniProt
VAR_021338
A
443
T
PCSK9_HUMAN
Polymorphism
28362263
A
A
443
T
36
UniProt
VAR_025456
R
469
W
PCSK9_HUMAN
Polymorphism
141502002
A
R
469
W
37
UniProt
VAR_021339
V
474
I
PCSK9_HUMAN
Polymorphism
562556
A
I
474
I
38
UniProt
VAR_025457
E
482
G
PCSK9_HUMAN
Polymorphism
---
A
E
482
G
39
UniProt
VAR_073657
E
482
Q
PCSK9_HUMAN
Unclassified
---
A
E
482
Q
40
UniProt
VAR_058534
R
496
W
PCSK9_HUMAN
Disease (HCHOLA3)
---
A
R
496
W
41
UniProt
VAR_025458
F
515
L
PCSK9_HUMAN
Polymorphism
---
A
F
515
L
42
UniProt
VAR_058535
A
522
T
PCSK9_HUMAN
Polymorphism
---
A
A
522
T
43
UniProt
VAR_058536
P
616
L
PCSK9_HUMAN
Polymorphism
---
A
P
616
L
44
UniProt
VAR_021341
Q
619
P
PCSK9_HUMAN
Polymorphism
28362277
A
Q
619
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: EGF_3 (E:293-332|-)
2: ASX_HYDROXYL (E:308-319|-)
3: EGF_2 (E:317-331|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_3
PS50026
EGF-like domain profile.
LDLR_HUMAN
314-353
354-393
1
E:293-332
-
2
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
LDLR_HUMAN
329-340
368-379
1
E:308-319
-
3
EGF_2
PS01186
EGF-like domain signature 2.
LDLR_HUMAN
338-352
377-392
1
E:317-331
-
[
close PROSITE info
]
Exons
(12, 13)
Info
All Exons
Exon 1.1b (- | P:61-69)
Exon 1.2 (- | P:70-133)
Exon 1.3 (A:153-172 | P:134-152)
Exon 1.4c (A:177-211 | -)
Exon 1.5 (A:220-267 | -)
Exon 1.6 (A:267-332 | -)
Exon 1.7a (A:333-394 | -)
Exon 1.8 (A:394-449 | -)
Exon 1.9 (A:453-501 | -)
Exon 1.10 (A:502-531 | -)
Exon 1.11 (A:602-621 | -)
Exon 1.12b (A:622-682 (gaps) | -)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4c
05: Boundary 1.4c/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7a
08: Boundary 1.7a/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12b
13: Boundary 1.12b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000302118
1b
ENSE00001884398
chr1:
55505221-55505717
497
PCSK9_HUMAN
1-69
69
1
-
P:61-69
-
9
1.2
ENST00000302118
2
ENSE00001279167
chr1:
55509516-55509707
192
PCSK9_HUMAN
70-133
64
1
-
P:70-133
-
64
1.3
ENST00000302118
3
ENSE00001279161
chr1:
55512196-55512319
124
PCSK9_HUMAN
134-175
42
2
A:153-172
P:134-152
20
19
1.4c
ENST00000302118
4c
ENSE00001279157
chr1:
55517951-55518084
134
PCSK9_HUMAN
175-219
45
1
A:177-211
-
35
-
1.5
ENST00000302118
5
ENSE00001279150
chr1:
55518323-55518464
142
PCSK9_HUMAN
220-267
48
1
A:220-267
-
48
-
1.6
ENST00000302118
6
ENSE00001279145
chr1:
55521666-55521862
197
PCSK9_HUMAN
267-332
66
1
A:267-332
-
66
-
1.7a
ENST00000302118
7a
ENSE00001156685
chr1:
55523004-55523187
184
PCSK9_HUMAN
333-394
62
1
A:333-394
-
62
-
1.8
ENST00000302118
8
ENSE00001139624
chr1:
55523709-55523882
174
PCSK9_HUMAN
394-452
59
1
A:394-449
-
56
-
1.9
ENST00000302118
9
ENSE00001279131
chr1:
55524172-55524320
149
PCSK9_HUMAN
452-501
50
1
A:453-501
-
49
-
1.10
ENST00000302118
10
ENSE00001338737
chr1:
55525159-55525336
178
PCSK9_HUMAN
502-561
60
1
A:502-531
-
30
-
1.11
ENST00000302118
11
ENSE00001338722
chr1:
55527048-55527229
182
PCSK9_HUMAN
561-621
61
1
A:602-621
-
20
-
1.12b
ENST00000302118
12b
ENSE00001922690
chr1:
55529042-55530525
1484
PCSK9_HUMAN
622-692
71
1
A:622-682 (gaps)
-
61
-
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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