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2C10
Biol. Unit 2
Info
Asym.Unit (484 KB)
Biol.Unit 1 (238 KB)
Biol.Unit 2 (240 KB)
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(1)
Title
:
THE STRUCTURE OF A TRUNCATED, SOLUBLE VERSION OF SEMICARBAZIDE-SENSITIVE AMINE OXIDASE
Authors
:
E. Jakobsson, G. J. Kleywegt
Date
:
09 Sep 05 (Deposition) - 20 Sep 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Semicarbazide-Sensitive Amine Oxidase, Vascular Adhesion, Protein-1, Ssao, Vap-1, Cell Adhesion, Glycoprotein, Metal- Binding, Oxidoreductase, Signal- Anchor, Tpq, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Jakobsson, J. Nilsson, D. Ogg, G. J. Kleywegt
Structure Of Human Semicarbazide-Sensitive Amine Oxidase/Vascular Adhesion Protein-1.
Acta Crystallogr. , Sect. D V. 61 1550 2005
[
close entry info
]
Hetero Components
(6, 25)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
4a: COPPER (II) ION (CUa)
4b: COPPER (II) ION (CUb)
4c: COPPER (II) ION (CUc)
4d: COPPER (II) ION (CUd)
5a: BETA-L-FUCOSE (FULa)
5b: BETA-L-FUCOSE (FULb)
5c: BETA-L-FUCOSE (FULc)
5d: BETA-L-FUCOSE (FULd)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
6c: ALPHA-D-MANNOSE (MANc)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
7ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
7l: N-ACETYL-D-GLUCOSAMINE (NAGl)
7m: N-ACETYL-D-GLUCOSAMINE (NAGm)
7n: N-ACETYL-D-GLUCOSAMINE (NAGn)
7o: N-ACETYL-D-GLUCOSAMINE (NAGo)
7p: N-ACETYL-D-GLUCOSAMINE (NAGp)
7q: N-ACETYL-D-GLUCOSAMINE (NAGq)
7r: N-ACETYL-D-GLUCOSAMINE (NAGr)
7s: N-ACETYL-D-GLUCOSAMINE (NAGs)
7t: N-ACETYL-D-GLUCOSAMINE (NAGt)
7u: N-ACETYL-D-GLUCOSAMINE (NAGu)
7v: N-ACETYL-D-GLUCOSAMINE (NAGv)
7w: N-ACETYL-D-GLUCOSAMINE (NAGw)
7x: N-ACETYL-D-GLUCOSAMINE (NAGx)
7y: N-ACETYL-D-GLUCOSAMINE (NAGy)
7z: N-ACETYL-D-GLUCOSAMINE (NAGz)
8a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
8b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
8c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
8d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
9a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
9b: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQb)
9c: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQc)
9d: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
CU
-1
Ligand/Ion
COPPER (II) ION
5
FUL
2
Ligand/Ion
BETA-L-FUCOSE
6
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
9
TPQ
2
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
[
close Hetero Component info
]
Sites
(33, 33)
Info
All Sites
01: CC4 (SOFTWARE)
02: CC5 (SOFTWARE)
03: CC6 (SOFTWARE)
04: CC7 (SOFTWARE)
05: CC8 (SOFTWARE)
06: CC9 (SOFTWARE)
07: DC1 (SOFTWARE)
08: DC2 (SOFTWARE)
09: DC3 (SOFTWARE)
10: DC4 (SOFTWARE)
11: DC5 (SOFTWARE)
12: DC6 (SOFTWARE)
13: DC7 (SOFTWARE)
14: DC8 (SOFTWARE)
15: DC9 (SOFTWARE)
16: EC1 (SOFTWARE)
17: EC2 (SOFTWARE)
18: EC3 (SOFTWARE)
19: EC4 (SOFTWARE)
20: EC5 (SOFTWARE)
21: EC6 (SOFTWARE)
22: EC7 (SOFTWARE)
23: EC8 (SOFTWARE)
24: EC9 (SOFTWARE)
25: FC9 (SOFTWARE)
26: GC1 (SOFTWARE)
27: GC2 (SOFTWARE)
28: GC3 (SOFTWARE)
29: GC4 (SOFTWARE)
30: GC5 (SOFTWARE)
31: GC6 (SOFTWARE)
32: GC7 (SOFTWARE)
33: GC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC4
SOFTWARE
NAG B:1765 , BMA B:1772 , HOH B:2139 , GLU D:536 , LYS D:672
BINDING SITE FOR RESIDUE NAG B1773
02
CC5
SOFTWARE
GLN C:133 , ASN C:137 , SER C:139 , VAL C:157 , NAG C:1763
BINDING SITE FOR RESIDUE NAG C1762
03
CC6
SOFTWARE
MET C:152 , ASP C:154 , NAG C:1762 , BMA C:1769
BINDING SITE FOR RESIDUE NAG C1763
04
CC7
SOFTWARE
NAG C:1763
BINDING SITE FOR RESIDUE BMA C1769
05
CC8
SOFTWARE
GLY C:284 , ASN C:592 , NAG C:1765 , FUL C:1766
BINDING SITE FOR RESIDUE NDG C1764
06
CC9
SOFTWARE
NDG C:1764
BINDING SITE FOR RESIDUE NAG C1765
07
DC1
SOFTWARE
GLU C:282 , NDG C:1764
BINDING SITE FOR RESIDUE FUL C1766
08
DC2
SOFTWARE
ASN C:232 , SER C:234 , NAG C:1770 , HOH C:2140 , TYR D:448 , SER D:449
BINDING SITE FOR RESIDUE NAG C1767
09
DC3
SOFTWARE
NAG C:1767 , HIS D:450 , ASP D:728
BINDING SITE FOR RESIDUE NAG C1770
10
DC4
SOFTWARE
ASN C:294
BINDING SITE FOR RESIDUE NAG C1768
11
DC5
SOFTWARE
PHE D:130 , GLN D:133 , ASN D:137 , SER D:139 , VAL D:157 , NAG D:1763
BINDING SITE FOR RESIDUE NAG D1762
12
DC6
SOFTWARE
NAG D:1762 , BMA D:1769
BINDING SITE FOR RESIDUE NAG D1763
13
DC7
SOFTWARE
NAG D:1763 , MAN D:1773
BINDING SITE FOR RESIDUE BMA D1769
14
DC8
SOFTWARE
BMA D:1769
BINDING SITE FOR RESIDUE MAN D1773
15
DC9
SOFTWARE
ASN D:592 , NAG D:1765 , FUL D:1766 , HOH D:2039 , HOH D:2136 , HOH D:2137
BINDING SITE FOR RESIDUE NDG D1764
16
EC1
SOFTWARE
NDG D:1764 , BMA D:1772 , NAG D:1774
BINDING SITE FOR RESIDUE NAG D1765
17
EC2
SOFTWARE
GLU D:282 , NDG D:1764
BINDING SITE FOR RESIDUE FUL D1766
18
EC3
SOFTWARE
NAG D:1765 , NAG D:1774 , MAN D:1775 , HOH D:2140
BINDING SITE FOR RESIDUE BMA D1772
19
EC4
SOFTWARE
BMA D:1772
BINDING SITE FOR RESIDUE MAN D1775
20
EC5
SOFTWARE
TYR C:448 , ARG D:206 , ASN D:232 , SER D:234 , NAG D:1771
BINDING SITE FOR RESIDUE NAG D1767
21
EC6
SOFTWARE
HIS C:450 , ARG C:726 , NAG D:1767 , HOH D:2139
BINDING SITE FOR RESIDUE NAG D1771
22
EC7
SOFTWARE
ASN D:294
BINDING SITE FOR RESIDUE NAG D1768
23
EC8
SOFTWARE
ASN D:666 , HOH D:2138
BINDING SITE FOR RESIDUE NAG D1770
24
EC9
SOFTWARE
GLU B:536 , NAG D:1765 , BMA D:1772 , HOH D:2142
BINDING SITE FOR RESIDUE NAG D1774
25
FC9
SOFTWARE
ASP C:529 , LEU C:530 , ASP C:531 , ASP C:673 , LEU C:674 , HOH C:2121
BINDING SITE FOR RESIDUE CA C1771
26
GC1
SOFTWARE
HIS C:520 , HIS C:522 , HIS C:684 , HOH C:2078
BINDING SITE FOR RESIDUE CU C1772
27
GC2
SOFTWARE
GLU C:572 , PHE C:663 , ASN C:665 , GLU C:667
BINDING SITE FOR RESIDUE CA C1773
28
GC3
SOFTWARE
ARG C:383 , GLN D:560
BINDING SITE FOR RESIDUE CL C1774
29
GC4
SOFTWARE
LYS C:252
BINDING SITE FOR RESIDUE CL C1775
30
GC5
SOFTWARE
ASP D:529 , LEU D:530 , ASP D:531 , ASP D:673 , LEU D:674 , HOH D:2092
BINDING SITE FOR RESIDUE CA D1776
31
GC6
SOFTWARE
HIS D:520 , HIS D:522 , HIS D:684 , HOH D:2068
BINDING SITE FOR RESIDUE CU D1777
32
GC7
SOFTWARE
GLU D:572 , PHE D:663 , ASN D:665 , GLU D:667 , HOH D:2113 , HOH D:2114
BINDING SITE FOR RESIDUE CA D1778
33
GC8
SOFTWARE
GLN C:560 , ARG D:383
BINDING SITE FOR RESIDUE CL D1779
[
close Site info
]
SAPs(SNPs)/Variants
(13, 26)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_052603 (R78Q, chain C/D, )
02: VAR_025027 (H167Y, chain C/D, )
03: VAR_052604 (V171M, chain C/D, )
04: VAR_052605 (H203R, chain C/D, )
05: VAR_012064 (Y317H, chain C/D, )
06: VAR_024343 (R329Q, chain C/D, )
07: VAR_025028 (I371T, chain C/D, )
08: VAR_025029 (A408S, chain C/D, )
09: VAR_025030 (R426H, chain C/D, )
10: VAR_025031 (R441W, chain C/D, )
11: VAR_025032 (A582T, chain C/D, )
12: VAR_025033 (G700S, chain C/D, )
13: VAR_025034 (A749V, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_052603
R
78
Q
AOC3_HUMAN
Polymorphism
402680
C/D
R
78
Q
02
UniProt
VAR_025027
H
167
Y
AOC3_HUMAN
Polymorphism
2228470
C/D
H
167
Y
03
UniProt
VAR_052604
V
171
M
AOC3_HUMAN
Polymorphism
408038
C/D
V
171
M
04
UniProt
VAR_052605
H
203
R
AOC3_HUMAN
Polymorphism
630079
C/D
H
203
R
05
UniProt
VAR_012064
Y
317
H
AOC3_HUMAN
Polymorphism
438287
C/D
Y
317
H
06
UniProt
VAR_024343
R
329
Q
AOC3_HUMAN
Polymorphism
2229595
C/D
R
329
Q
07
UniProt
VAR_025028
I
371
T
AOC3_HUMAN
Polymorphism
35097308
C/D
I
371
T
08
UniProt
VAR_025029
A
408
S
AOC3_HUMAN
Polymorphism
35643019
C/D
A
408
S
09
UniProt
VAR_025030
R
426
H
AOC3_HUMAN
Polymorphism
33986943
C/D
R
426
H
10
UniProt
VAR_025031
R
441
W
AOC3_HUMAN
Polymorphism
2229596
C/D
R
441
W
11
UniProt
VAR_025032
A
582
T
AOC3_HUMAN
Polymorphism
34987927
C/D
A
582
T
12
UniProt
VAR_025033
G
700
S
AOC3_HUMAN
Polymorphism
477207
C/D
G
700
S
13
UniProt
VAR_025034
A
749
V
AOC3_HUMAN
Polymorphism
34012919
C/D
A
749
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: COPPER_AMINE_OXID_1 (C:460-473,D:460-473)
2: COPPER_AMINE_OXID_2 (C:679-692,D:679-692)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COPPER_AMINE_OXID_1
PS01164
Copper amine oxidase topaquinone signature.
AOC3_HUMAN
460-473
2
-
-
C:460-473
D:460-473
2
COPPER_AMINE_OXID_2
PS01165
Copper amine oxidase copper-binding site signature.
AOC3_HUMAN
679-692
2
-
-
C:679-692
D:679-692
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2c10A01 (A:41-165)
1b: CATH_2c10D01 (D:39-165)
1c: CATH_2c10A02 (A:166-297)
1d: CATH_2c10B02 (B:166-297)
1e: CATH_2c10C02 (C:166-297)
1f: CATH_2c10D02 (D:166-297)
1g: CATH_2c10C01 (C:41-165)
1h: CATH_2c10B01 (B:39-165)
2a: CATH_2c10A03 (A:322-728)
2b: CATH_2c10D03 (D:322-728)
2c: CATH_2c10B03 (B:322-728)
2d: CATH_2c10C03 (C:322-728)
View:
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Classes
(
)
(
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.40, no name defined]
(77)
Human (Homo sapiens)
(8)
1a
2c10A01
A:41-165
1b
2c10D01
D:39-165
1c
2c10A02
A:166-297
1d
2c10B02
B:166-297
1e
2c10C02
C:166-297
1f
2c10D02
D:166-297
1g
2c10C01
C:41-165
1h
2c10B01
B:39-165
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
Copper amine oxidase, Domain 3
(74)
Human (Homo sapiens)
(8)
2a
2c10A03
A:322-728
2b
2c10D03
D:322-728
2c
2c10B03
B:322-728
2d
2c10C03
C:322-728
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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