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1C1Z
Asym. Unit
Info
Asym.Unit (63 KB)
Biol.Unit 1 (58 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN BETA-2-GLYCOPROTEIN-I (APOLIPOPROTEIN-H)
Authors
:
R. Schwarzenbacher, K. Zeth, K. Diederichs, A. Gries, G. M. Kostner, P. R. Prassl
Date
:
22 Jul 99 (Deposition) - 19 Nov 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.87
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Glycoprotein, Short Consensus Repeat, Scr, Sushi Domain, Complement Control Protein Module, Ccp, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Schwarzenbacher, K. Zeth, K. Diederichs, A. Gries, G. M. Kostner, P. Laggner, R. Prassl
Crystal Structure Of Human Beta2-Glycoprotein I: Implications For Phospholipid Binding And The Antiphospholipid Syndrome.
Embo J. V. 18 6228 1999
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
4c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
4d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
4
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:143 , NDG A:328
BINDING SITE FOR RESIDUE NDG A 327
02
AC2
SOFTWARE
NDG A:327
BINDING SITE FOR RESIDUE NDG A 328
03
AC3
SOFTWARE
ASN A:164
BINDING SITE FOR RESIDUE NDG A 329
04
AC4
SOFTWARE
PRO A:5 , LYS A:6 , ASN A:174 , TRP A:175 , LYS A:177 , NDG A:331
BINDING SITE FOR RESIDUE NAG A 330
05
AC5
SOFTWARE
ASP A:8 , HIS A:172 , NAG A:330 , BMA A:332
BINDING SITE FOR RESIDUE NDG A 331
06
AC6
SOFTWARE
NDG A:331 , BMA A:333 , MAN A:334
BINDING SITE FOR RESIDUE BMA A 332
07
AC7
SOFTWARE
BMA A:332
BINDING SITE FOR RESIDUE BMA A 333
08
AC8
SOFTWARE
BMA A:332
BINDING SITE FOR RESIDUE MAN A 334
09
AC9
SOFTWARE
LEU A:232 , ASN A:234 , TRP A:235 , SER A:236 , NAG A:336
BINDING SITE FOR RESIDUE NAG A 335
10
BC1
SOFTWARE
NAG A:335 , MAN A:337
BINDING SITE FOR RESIDUE NAG A 336
11
BC2
SOFTWARE
NAG A:336
BINDING SITE FOR RESIDUE MAN A 337
[
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SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_008169 (S88N, chain A, )
2: VAR_019155 (R135H, chain A, )
3: VAR_000673 (L247L, chain A, )
4: VAR_008170 (C306G, chain A, )
5: VAR_008171 (W316S, 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
L
247
L
4
UniProt
VAR_008170
C
325
G
APOH_HUMAN
Polymorphism
1801689
A
C
306
G
5
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: SUSHI (A:2-62|A:63-120|A:121-183|A:184-24...)
;
View:
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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)
View:
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Label:
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:
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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
18
[
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SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1c1za1 (A:1-62)
1b: SCOP_d1c1za2 (A:63-120)
1c: SCOP_d1c1za3 (A:121-183)
1d: SCOP_d1c1za4 (A:184-243)
1e: SCOP_d1c1za5 (A:244-326)
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(
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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
d1c1za1
A:1-62
1b
d1c1za2
A:63-120
1c
d1c1za3
A:121-183
1d
d1c1za4
A:184-243
1e
d1c1za5
A:244-326
[
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1c1zA01 (A:1-62)
1b: CATH_1c1zA03 (A:122-183)
1c: CATH_1c1zA04 (A:184-243)
1d: CATH_1c1zA02 (A:63-121)
1e: CATH_1c1zA05 (A:244-325)
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)
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(
)
(
)
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
1c1zA01
A:1-62
1b
1c1zA03
A:122-183
1c
1c1zA04
A:184-243
1d
1c1zA02
A:63-121
1e
1c1zA05
A:244-325
[
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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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Chain A
Asymmetric Unit 1
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