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1QUB
Asym. Unit
Info
Asym.Unit (60 KB)
Biol.Unit 1 (55 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLYCOPROTEIN I PURIFIED FROM BLOOD PLASMA
Authors
:
B. Bouma, Ph. G. De Groot, J. M. H. Van Den Elsen, R. B. G. Ravelli, A. Sc M. J. A. Simmelink, R. H. W. M. Derksen, J. Kroon, P. Gros
Date
:
01 Jul 99 (Deposition) - 08 Oct 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Short Consensus Repeat, Sushi, Complement Control Protein, N- Glycosylation, Multi-Domain, Membrane Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
B. Bouma, P. G. De Groot, J. M. Van Den Elsen, R. B. Ravelli, A. Schouten, M. J. Simmelink, R. H. Derksen, J. Kroon, P. Gros
Adhesion Mechanism Of Human Beta(2)-Glycoprotein I To Phospholipids Based On Its Crystal Structure.
Embo J. V. 18 5166 1999
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: ALPHA-D-MANNOSE (MANa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
2
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:143
BINDING SITE FOR RESIDUE NAG A 1431
2
AC2
SOFTWARE
ASN A:164 , THR A:166 , THR A:168
BINDING SITE FOR RESIDUE NAG A 1641
3
AC3
SOFTWARE
PRO A:5 , ASN A:174 , TRP A:175 , HOH A:624 , NAG A:1742
BINDING SITE FOR RESIDUE NAG A 1741
4
AC4
SOFTWARE
ASP A:8 , NAG A:1741 , MAN A:1743
BINDING SITE FOR RESIDUE NAG A 1742
5
AC5
SOFTWARE
NAG A:1742
BINDING SITE FOR RESIDUE MAN A 1743
6
AC6
SOFTWARE
ASN A:234 , SER A:236 , NAG A:2342
BINDING SITE FOR RESIDUE NAG A 2341
7
AC7
SOFTWARE
NAG A:2341
BINDING SITE FOR RESIDUE NAG A 2342
[
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_008169 (S88N, chain A, )
2: VAR_019155 (R135H, chain A, )
3: VAR_000673 (V247L, chain A, )
4: VAR_008170 (C306G, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_008169
S
107
N
APOH_HUMAN
Polymorphism
1801692
A
S
88
N
2
UniProt
VAR_019155
R
154
H
APOH_HUMAN
Polymorphism
8178847
A
R
135
H
3
UniProt
VAR_000673
V
266
L
APOH_HUMAN
Polymorphism
4581
A
V
247
L
4
UniProt
VAR_008170
C
325
G
APOH_HUMAN
Polymorphism
1801689
A
C
306
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: SUSHI (A:2-62|A:63-120|A:121-183|A:184-24...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUSHI
PS50923
Sushi/CCP/SCR domain profile.
APOH_HUMAN
21-81
82-139
140-202
203-262
4
A:2-62
A:63-120
A:121-183
A:184-243
[
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Exons
(8, 8)
Info
All Exons
Exon 1.1 (A:1-3)
Exon 1.2 (A:3-62)
Exon 1.3 (A:62-94)
Exon 1.4 (A:94-120)
Exon 1.5 (A:120-183)
Exon 1.6 (A:183-243)
Exon 1.7 (A:243-309)
Exon 1.8 (A:309-326 (gaps))
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/1.8
9: 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
1
A:1-3
3
1.2
ENST00000205948
2
ENSE00000742667
chr17:
64224314-64224138
177
APOH_HUMAN
22-81
60
1
A:3-62
60
1.3
ENST00000205948
3
ENSE00000742665
chr17:
64222242-64222146
97
APOH_HUMAN
81-113
33
1
A:62-94
33
1.4
ENST00000205948
4
ENSE00000742663
chr17:
64219892-64219816
77
APOH_HUMAN
113-139
27
1
A:94-120
27
1.5
ENST00000205948
5
ENSE00000742652
chr17:
64216860-64216672
189
APOH_HUMAN
139-202
64
1
A:120-183
64
1.6
ENST00000205948
6
ENSE00000584156
chr17:
64213085-64212906
180
APOH_HUMAN
202-262
61
1
A:183-243
61
1.7
ENST00000205948
7
ENSE00000742648
chr17:
64210768-64210571
198
APOH_HUMAN
262-328
67
1
A:243-309
67
1.8
ENST00000205948
8
ENSE00000837173
chr17:
64208306-64208148
159
APOH_HUMAN
328-345
18
1
A:309-326 (gaps)
18
[
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SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1quba1 (A:1-62)
1b: SCOP_d1quba2 (A:63-120)
1c: SCOP_d1quba3 (A:121-183)
1d: SCOP_d1quba4 (A:184-243)
1e: SCOP_d1quba5 (A:244-326)
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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
d1quba1
A:1-62
1b
d1quba2
A:63-120
1c
d1quba3
A:121-183
1d
d1quba4
A:184-243
1e
d1quba5
A:244-326
[
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1qubA01 (A:1-62)
1b: CATH_1qubA03 (A:122-183)
1c: CATH_1qubA04 (A:184-243)
1d: CATH_1qubA02 (A:63-121)
1e: CATH_1qubA05 (A:244-326)
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Topologies
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)
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
1qubA01
A:1-62
1b
1qubA03
A:122-183
1c
1qubA04
A:184-243
1d
1qubA02
A:63-121
1e
1qubA05
A:244-326
[
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Pfam Domains
(2, 5)
Info
all PFAM domains
1a: PFAM_Sushi_1qubA01 (A:186-241)
1b: PFAM_Sushi_1qubA02 (A:186-241)
1c: PFAM_Sushi_1qubA03 (A:186-241)
1d: PFAM_Sushi_1qubA04 (A:186-241)
2a: PFAM_Sushi_2_1qubA05 (A:242-310)
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Clans
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Organisms
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(
)
Clan
:
no clan defined [family: Sushi]
(50)
Family
:
Sushi
(50)
Homo sapiens (Human)
(42)
1a
Sushi-1qubA01
A:186-241
1b
Sushi-1qubA02
A:186-241
1c
Sushi-1qubA03
A:186-241
1d
Sushi-1qubA04
A:186-241
Clan
:
no clan defined [family: Sushi_2]
(3)
Family
:
Sushi_2
(3)
Homo sapiens (Human)
(3)
2a
Sushi_2-1qubA05
A:242-310
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Chain A
Asymmetric Unit 1
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