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3H42
Asym. Unit
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Asym.Unit (173 KB)
Biol.Unit 1 (168 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PCSK9 IN COMPLEX WITH FAB FROM LDLR COMPETITIVE ANTIBODY
Authors
:
D. E. Piper, N. P. C. Walker, W. G. Romanow, S. T. Thibault, M. M. Tsai, E. Y
Date
:
17 Apr 09 (Deposition) - 05 May 09 (Release) - 21 Jul 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,H,L
Biol. Unit 1: A,B,H,L (1x)
Keywords
:
Hydrolase, Protein Fab Complex, Autocatalytic Cleavage, Cholesterol Metabolism, Disease Mutation, Disulfide Bond, Glycoprotein, Lipid Metabolism, Phosphoprotein, Protease, Secreted, Serine Protease, Steroid Metabolism, Zymogen, Hydrolase-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. C. Chan, D. E. Piper, Q. Cao, D. Liu, C. King, W. Wang, J. Tang, Q. Liu, J. Higbee, Z. Xia, Y. Di, S. Shetterly, Z. Arimura, H. Salomonis, W. G. Romanow, S. T. Thibault, R. Zhang, P. Cao, X. P. Yang, T. Yu, M. Lu, M. W. Retter, G. Kwon, K. Henne, O. Pan, M. M. Tsai, B. Fuchslocher, E. Yang, L. Zhou, K. J. Lee, M. Daris, J. Sheng, Y. Wang, W. D. Shen, W. C. Yeh, M. Emery, N. P. Walker, B. Shan, M. Schwarz, S. M. Jackson
From The Cover: A Proprotein Convertase Subtilisin/Kexin Type 9 Neutralizing Antibody Reduces Serum Cholesterol In Mice And Nonhuman Primates.
Proc. Natl. Acad. Sci. Usa V. 106 9820 2009
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
1
Ligand/Ion
SODIUM ION
[
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]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH B:106 , ALA B:328 , ALA B:330 , VAL B:333 , THR B:335 , CYS B:358 , ASP B:360
BINDING SITE FOR RESIDUE NA B 1
[
close Site info
]
SAPs(SNPs)/Variants
(33, 33)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_058520 (T77I, chain A, )
02: VAR_058521 (R93C, chain A, )
03: VAR_058522 (G106R, chain A, )
04: VAR_058523 (V114A, chain A, )
05: VAR_017199 (S127R, chain A, )
06: VAR_058524 (D129G, chain A, )
07: VAR_058525 (N157K, chain B, )
08: VAR_058526 (R215H, chain B, )
09: VAR_017200 (F216L, chain B, )
10: VAR_058527 (R218S, chain B, )
11: VAR_058528 (Q219E, chain B, )
12: VAR_025452 (R237W, chain B, )
13: VAR_058529 (A239D, chain B, )
14: VAR_025453 (L253F, chain B, )
15: VAR_058530 (R357H, chain B, )
16: VAR_058531 (D374H, chain B, )
17: VAR_058532 (D374Y, chain B, )
18: VAR_025454 (H391N, chain B, )
19: VAR_067282 (G394S, chain B, )
20: VAR_025455 (H417Q, chain B, )
21: VAR_021337 (N425S, chain B, )
22: VAR_021338 (A443T, chain B, )
23: VAR_025456 (R469W, chain B, )
24: VAR_021339 (I474I, chain B, )
25: VAR_025457 (E482G, chain B, )
26: VAR_073657 (E482Q, chain B, )
27: VAR_058534 (R496W, chain B, )
28: VAR_025458 (F515L, chain B, )
29: VAR_058535 (A522T, chain B, )
30: VAR_021340 (H553R, chain B, )
31: VAR_025459 (Q554E, chain B, )
32: VAR_058536 (P616L, chain B, )
33: VAR_021341 (Q619P, chain B, )
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
---
A
T
77
I
02
UniProt
VAR_058521
R
93
C
PCSK9_HUMAN
Polymorphism
151193009
A
R
93
C
03
UniProt
VAR_058522
G
106
R
PCSK9_HUMAN
Polymorphism
---
A
G
106
R
04
UniProt
VAR_058523
V
114
A
PCSK9_HUMAN
Polymorphism
---
A
V
114
A
05
UniProt
VAR_017199
S
127
R
PCSK9_HUMAN
Disease (HCHOLA3)
28942111
A
S
127
R
06
UniProt
VAR_058524
D
129
G
PCSK9_HUMAN
Disease (HCHOLA3)
---
A
D
129
G
07
UniProt
VAR_058525
N
157
K
PCSK9_HUMAN
Polymorphism
---
B
N
157
K
08
UniProt
VAR_058526
R
215
H
PCSK9_HUMAN
Disease (HCHOLA3)
---
B
R
215
H
09
UniProt
VAR_017200
F
216
L
PCSK9_HUMAN
Disease (HCHOLA3)
28942112
B
F
216
L
10
UniProt
VAR_058527
R
218
S
PCSK9_HUMAN
Disease (HCHOLA3)
---
B
R
218
S
11
UniProt
VAR_058528
Q
219
E
PCSK9_HUMAN
Polymorphism
---
B
Q
219
E
12
UniProt
VAR_025452
R
237
W
PCSK9_HUMAN
Polymorphism
---
B
R
237
W
13
UniProt
VAR_058529
A
239
D
PCSK9_HUMAN
Polymorphism
---
B
A
239
D
14
UniProt
VAR_025453
L
253
F
PCSK9_HUMAN
Polymorphism
28362270
B
L
253
F
15
UniProt
VAR_058530
R
357
H
PCSK9_HUMAN
Disease (HCHOLA3)
---
B
R
357
H
16
UniProt
VAR_058531
D
374
H
PCSK9_HUMAN
Disease (HCHOLA3)
---
B
D
374
H
17
UniProt
VAR_058532
D
374
Y
PCSK9_HUMAN
Disease (HCHOLA3)
---
B
D
374
Y
18
UniProt
VAR_025454
H
391
N
PCSK9_HUMAN
Polymorphism
---
B
H
391
N
19
UniProt
VAR_067282
G
394
S
PCSK9_HUMAN
Unclassified
---
B
G
394
S
20
UniProt
VAR_025455
H
417
Q
PCSK9_HUMAN
Polymorphism
143275858
B
H
417
Q
21
UniProt
VAR_021337
N
425
S
PCSK9_HUMAN
Polymorphism
28362261
B
N
425
S
22
UniProt
VAR_021338
A
443
T
PCSK9_HUMAN
Polymorphism
28362263
B
A
443
T
23
UniProt
VAR_025456
R
469
W
PCSK9_HUMAN
Polymorphism
141502002
B
R
469
W
24
UniProt
VAR_021339
V
474
I
PCSK9_HUMAN
Polymorphism
562556
B
I
474
I
25
UniProt
VAR_025457
E
482
G
PCSK9_HUMAN
Polymorphism
---
B
E
482
G
26
UniProt
VAR_073657
E
482
Q
PCSK9_HUMAN
Unclassified
---
B
E
482
Q
27
UniProt
VAR_058534
R
496
W
PCSK9_HUMAN
Disease (HCHOLA3)
---
B
R
496
W
28
UniProt
VAR_025458
F
515
L
PCSK9_HUMAN
Polymorphism
---
B
F
515
L
29
UniProt
VAR_058535
A
522
T
PCSK9_HUMAN
Polymorphism
---
B
A
522
T
30
UniProt
VAR_021340
H
553
R
PCSK9_HUMAN
Polymorphism
28362270
B
H
553
R
31
UniProt
VAR_025459
Q
554
E
PCSK9_HUMAN
Polymorphism
149311926
B
Q
554
E
32
UniProt
VAR_058536
P
616
L
PCSK9_HUMAN
Polymorphism
---
B
P
616
L
33
UniProt
VAR_021341
Q
619
P
PCSK9_HUMAN
Polymorphism
28362277
B
Q
619
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(12, 13)
Info
All Exons
Exon 1.1b (A:61-69 | -)
Exon 1.2 (A:70-133 | -)
Exon 1.3 (A:134-152 | B:153-171 (gaps))
Exon 1.4c (- | B:179-219)
Exon 1.5 (- | B:220-267)
Exon 1.6 (- | B:267-332)
Exon 1.7a (- | B:333-394)
Exon 1.8 (- | B:394-449)
Exon 1.9 (- | B:453-501)
Exon 1.10 (- | B:502-561)
Exon 1.11 (- | B:561-621 (gaps))
Exon 1.12b (- | B: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
A:61-69
-
9
-
1.2
ENST00000302118
2
ENSE00001279167
chr1:
55509516-55509707
192
PCSK9_HUMAN
70-133
64
1
A:70-133
-
64
-
1.3
ENST00000302118
3
ENSE00001279161
chr1:
55512196-55512319
124
PCSK9_HUMAN
134-175
42
2
A:134-152
B:153-171 (gaps)
19
19
1.4c
ENST00000302118
4c
ENSE00001279157
chr1:
55517951-55518084
134
PCSK9_HUMAN
175-219
45
1
-
B:179-219
-
41
1.5
ENST00000302118
5
ENSE00001279150
chr1:
55518323-55518464
142
PCSK9_HUMAN
220-267
48
1
-
B:220-267
-
48
1.6
ENST00000302118
6
ENSE00001279145
chr1:
55521666-55521862
197
PCSK9_HUMAN
267-332
66
1
-
B:267-332
-
66
1.7a
ENST00000302118
7a
ENSE00001156685
chr1:
55523004-55523187
184
PCSK9_HUMAN
333-394
62
1
-
B:333-394
-
62
1.8
ENST00000302118
8
ENSE00001139624
chr1:
55523709-55523882
174
PCSK9_HUMAN
394-452
59
1
-
B:394-449
-
56
1.9
ENST00000302118
9
ENSE00001279131
chr1:
55524172-55524320
149
PCSK9_HUMAN
452-501
50
1
-
B:453-501
-
49
1.10
ENST00000302118
10
ENSE00001338737
chr1:
55525159-55525336
178
PCSK9_HUMAN
502-561
60
1
-
B:502-561
-
60
1.11
ENST00000302118
11
ENSE00001338722
chr1:
55527048-55527229
182
PCSK9_HUMAN
561-621
61
1
-
B:561-621 (gaps)
-
61
1.12b
ENST00000302118
12b
ENSE00001922690
chr1:
55529042-55530525
1484
PCSK9_HUMAN
622-692
71
1
-
B:622-682 (gaps)
-
61
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3h42l2 (L:113-214)
2a: SCOP_d3h42l1 (L:1-112)
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Folds
(
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(
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
1a
d3h42l2
L:113-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
automated matches
(311)
Human (Homo sapiens) [TaxId: 9606]
(85)
2a
d3h42l1
L:1-112
[
close SCOP info
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3h42H02 (H:124-224)
1b: CATH_3h42H01 (H:1-123)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
3h42H02
H:124-224
1b
3h42H01
H:1-123
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Pfam Domains
(0, 0)
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all PFAM domains
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