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2KRI
Asym. Unit
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Asym.Unit (23 KB)
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(1)
Title
:
STRUCTURE OF A COMPLEX BETWEEN DOMAIN V OF BETA2-GLYCOPROTEIN I AND THE FOURTH LIGAND-BINDING MODULE FROM LDLR DETERMINED WITH HADDOCK
Authors
:
N. Beglova
Date
:
18 Dec 09 (Deposition) - 31 Mar 10 (Release) - 31 Mar 10 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A,B
Keywords
:
Antiphospholipid Syndrome, Thrombosis, Ldlr, Receptor, Disulfide Bond, Glycoprotein, Heparin-Binding, Sushi, Protein Binding-Endocytosis Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. J. Lee, A. De Biasio, N. Beglova
Mode Of Interaction Between Beta2Gpi And Lipoprotein Receptors Suggests Mutually Exclusive Binding Of Beta2Gpi To The Receptors And Anionic Phospholipids.
Structure V. 18 366 2010
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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
TRP B:144 , ASP B:147 , ASP B:149 , ASP B:151 , ASP B:157 , GLU B:158
BINDING SITE FOR RESIDUE CA B 166
[
close Site info
]
SAPs(SNPs)/Variants
(20, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_072829 (C127Y, chain B, )
02: VAR_005319 (C134G, chain B, )
03: VAR_072830 (C134Y, chain B, )
04: VAR_005320 (C139Y, chain B, )
05: VAR_072831 (D147A, chain B, )
06: VAR_005321 (D147H, chain B, )
07: VAR_005322 (D147N, chain B, )
08: VAR_005323 (D147Y, chain B, )
09: VAR_013950 (D151H, chain B, )
10: VAR_072832 (D151N, chain B, )
11: VAR_005324 (C152R, chain B, )
12: VAR_005325 (C152W, chain B, )
13: VAR_005326 (D154N, chain B, )
14: VAR_007981 (D154Y, chain B, )
15: VAR_005327 (S156L, chain B, )
16: VAR_072833 (C163W, chain B, )
17: VAR_013951 (C163Y, chain B, )
18: VAR_000673 (L247L, chain A, )
19: VAR_008170 (C306G, chain A, )
20: VAR_008171 (W316S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_072829
C
148
Y
LDLR_HUMAN
Disease (FH)
---
B
C
127
Y
02
UniProt
VAR_005319
C
155
G
LDLR_HUMAN
Unclassified
---
B
C
134
G
03
UniProt
VAR_072830
C
155
Y
LDLR_HUMAN
Disease (FH)
---
B
C
134
Y
04
UniProt
VAR_005320
C
160
Y
LDLR_HUMAN
Unclassified
---
B
C
139
Y
05
UniProt
VAR_072831
D
168
A
LDLR_HUMAN
Unclassified
---
B
D
147
A
06
UniProt
VAR_005321
D
168
H
LDLR_HUMAN
Disease (FH)
---
B
D
147
H
07
UniProt
VAR_005322
D
168
N
LDLR_HUMAN
Disease (FH)
---
B
D
147
N
08
UniProt
VAR_005323
D
168
Y
LDLR_HUMAN
Disease (FH)
---
B
D
147
Y
09
UniProt
VAR_013950
D
172
H
LDLR_HUMAN
Unclassified
---
B
D
151
H
10
UniProt
VAR_072832
D
172
N
LDLR_HUMAN
Disease (FH)
---
B
D
151
N
11
UniProt
VAR_005324
C
173
R
LDLR_HUMAN
Unclassified
---
B
C
152
R
12
UniProt
VAR_005325
C
173
W
LDLR_HUMAN
Disease (FH)
---
B
C
152
W
13
UniProt
VAR_005326
D
175
N
LDLR_HUMAN
Disease (FH)
---
B
D
154
N
14
UniProt
VAR_007981
D
175
Y
LDLR_HUMAN
Disease (FH)
---
B
D
154
Y
15
UniProt
VAR_005327
S
177
L
LDLR_HUMAN
Disease (FH)
---
B
S
156
L
16
UniProt
VAR_072833
C
184
W
LDLR_HUMAN
Disease (FH)
---
B
C
163
W
17
UniProt
VAR_013951
C
184
Y
LDLR_HUMAN
Disease (FH)
---
B
C
163
Y
18
UniProt
VAR_000673
V
266
L
APOH_HUMAN
Polymorphism
4581
A
L
247
L
19
UniProt
VAR_008170
C
325
G
APOH_HUMAN
Polymorphism
1801689
A
C
306
G
20
UniProt
VAR_008171
W
335
S
APOH_HUMAN
Polymorphism
1801690
A
W
316
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: LDLRA_2 (-|-|-|B:126-163|-|-|-)
2: LDLRA_1 (-|-|-|B:139-163|-|-|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LDLRA_2
PS50068
LDL-receptor class A (LDLRA) domain profile.
LDLR_HUMAN
26-64
67-105
108-144
147-185
196-232
235-271
275-314
1
-
-
-
B:126-163
-
-
-
2
LDLRA_1
PS01209
LDL-receptor class A (LDLRA) domain signature.
LDLR_HUMAN
39-63
82-104
121-143
160-184
209-231
248-270
289-313
1
-
-
-
B:139-163
-
-
-
[
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Exons
(2, 2)
Info
All Exons
Exon 1.7 (A:245-309)
Exon 1.8 (A:309-326)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.6/1.7
2: Boundary 1.7/1.8
3: Boundary 1.8/-
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
1.1
ENST00000205948
1
ENSE00001149177
chr17:
64225556-64225434
123
APOH_HUMAN
1-22
22
0
-
-
1.2
ENST00000205948
2
ENSE00000742667
chr17:
64224314-64224138
177
APOH_HUMAN
22-81
60
0
-
-
1.3
ENST00000205948
3
ENSE00000742665
chr17:
64222242-64222146
97
APOH_HUMAN
81-113
33
0
-
-
1.4
ENST00000205948
4
ENSE00000742663
chr17:
64219892-64219816
77
APOH_HUMAN
113-139
27
0
-
-
1.5
ENST00000205948
5
ENSE00000742652
chr17:
64216860-64216672
189
APOH_HUMAN
139-202
64
0
-
-
1.6
ENST00000205948
6
ENSE00000584156
chr17:
64213085-64212906
180
APOH_HUMAN
202-262
61
0
-
-
1.7
ENST00000205948
7
ENSE00000742648
chr17:
64210768-64210571
198
APOH_HUMAN
262-328
67
1
A:245-309
65
1.8
ENST00000205948
8
ENSE00000837173
chr17:
64208306-64208148
159
APOH_HUMAN
328-345
18
1
A:309-326
18
[
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]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2kria_ (A:)
2a: SCOP_d2krib_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Complement control module/SCR domain
(70)
Superfamily
:
Complement control module/SCR domain
(70)
Family
:
Complement control module/SCR domain
(67)
Protein domain
:
beta2-glycoprotein I
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d2kria_
A:
Fold
:
LDL receptor-like module
(20)
Superfamily
:
LDL receptor-like module
(20)
Family
:
LDL receptor-like module
(19)
Protein domain
:
Ligand-binding domain of low-density lipoprotein receptor
(13)
Human (Homo sapiens) [TaxId: 9606]
(13)
2a
d2krib_
B:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2kriA00 (A:245-326)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Complement Module; domain 1
(62)
Homologous Superfamily
:
Complement Module, domain 1
(60)
Human (Homo sapiens)
(46)
1a
2kriA00
A:245-326
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Ldl_recept_a_2kriB01 (B:126-163)
2a: PFAM_Sushi_2_2kriA01 (A:245-326)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Ldl_recept_a]
(10)
Family
:
Ldl_recept_a
(10)
Homo sapiens (Human)
(9)
1a
Ldl_recept_a-2kriB01
B:126-163
Clan
:
no clan defined [family: Sushi_2]
(3)
Family
:
Sushi_2
(3)
Homo sapiens (Human)
(3)
2a
Sushi_2-2kriA01
A:245-326
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]
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