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2C10
Biol. Unit 1
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, 24)
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
1
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
(31, 31)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: EC9 (SOFTWARE)
24: FC1 (SOFTWARE)
25: FC2 (SOFTWARE)
26: FC3 (SOFTWARE)
27: FC4 (SOFTWARE)
28: FC5 (SOFTWARE)
29: FC6 (SOFTWARE)
30: FC7 (SOFTWARE)
31: FC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:130 , GLN A:133 , ASN A:137 , SER A:139 , VAL A:157 , NAG A:1763 , HOH A:2020
BINDING SITE FOR RESIDUE NAG A1762
02
AC2
SOFTWARE
MET A:152 , NAG A:1762 , BMA A:1769
BINDING SITE FOR RESIDUE NAG A1763
03
AC3
SOFTWARE
NAG A:1763
BINDING SITE FOR RESIDUE BMA A1769
04
AC4
SOFTWARE
ASN A:592 , NAG A:1765 , FUL A:1766 , HOH A:2051
BINDING SITE FOR RESIDUE NDG A1764
05
AC5
SOFTWARE
NDG A:1764
BINDING SITE FOR RESIDUE NAG A1765
06
AC6
SOFTWARE
GLU A:282 , NDG A:1764
BINDING SITE FOR RESIDUE FUL A1766
07
AC7
SOFTWARE
ARG A:206 , VAL A:209 , ASN A:232 , NAG A:1770 , TYR B:448
BINDING SITE FOR RESIDUE NAG A1767
08
AC8
SOFTWARE
NAG A:1767 , HIS B:450
BINDING SITE FOR RESIDUE NAG A1770
09
AC9
SOFTWARE
ASN A:294 , THR A:296 , HOH A:2141
BINDING SITE FOR RESIDUE NAG A1768
10
BC1
SOFTWARE
PHE B:130 , GLN B:133 , ASN B:137 , SER B:139 , NAG B:1763 , HOH B:2014
BINDING SITE FOR RESIDUE NAG B1762
11
BC2
SOFTWARE
NAG B:1762 , BMA B:1769
BINDING SITE FOR RESIDUE NAG B1763
12
BC3
SOFTWARE
NAG B:1763
BINDING SITE FOR RESIDUE BMA B1769
13
BC4
SOFTWARE
ASN B:592 , NAG B:1765 , FUL B:1766 , HOH B:2137 , HOH B:2138
BINDING SITE FOR RESIDUE NDG B1764
14
BC5
SOFTWARE
NDG B:1764 , FUL B:1766 , BMA B:1772 , NAG B:1773
BINDING SITE FOR RESIDUE NAG B1765
15
BC6
SOFTWARE
GLU B:282 , NDG B:1764 , NAG B:1765
BINDING SITE FOR RESIDUE FUL B1766
16
BC7
SOFTWARE
NAG B:1765 , NAG B:1773 , MAN B:1774
BINDING SITE FOR RESIDUE BMA B1772
17
BC8
SOFTWARE
HIS B:203 , BMA B:1772
BINDING SITE FOR RESIDUE MAN B1774
18
BC9
SOFTWARE
TYR A:448 , SER A:449 , ARG B:206 , ASN B:232 , SER B:234 , NAG B:1771
BINDING SITE FOR RESIDUE NAG B1767
19
CC1
SOFTWARE
HIS A:450 , ASP A:728 , NAG B:1767
BINDING SITE FOR RESIDUE NAG B1771
20
CC2
SOFTWARE
ASN B:294
BINDING SITE FOR RESIDUE NAG B1768
21
CC3
SOFTWARE
ASN B:666
BINDING SITE FOR RESIDUE NAG B1770
22
CC4
SOFTWARE
NAG B:1765 , BMA B:1772 , HOH B:2139 , GLU D:536 , LYS D:672
BINDING SITE FOR RESIDUE NAG B1773
23
EC9
SOFTWARE
GLU B:536 , NAG D:1765 , BMA D:1772 , HOH D:2142
BINDING SITE FOR RESIDUE NAG D1774
24
FC1
SOFTWARE
ASP A:529 , LEU A:530 , ASP A:531 , ASP A:673 , LEU A:674 , HOH A:2105
BINDING SITE FOR RESIDUE CA A1771
25
FC2
SOFTWARE
HIS A:520 , HIS A:522 , HIS A:684 , HOH A:2089
BINDING SITE FOR RESIDUE CU A1772
26
FC3
SOFTWARE
GLU A:572 , PHE A:663 , ASN A:665 , GLU A:667 , HOH A:2125
BINDING SITE FOR RESIDUE CA A1773
27
FC4
SOFTWARE
ARG A:383 , GLN B:560
BINDING SITE FOR RESIDUE CL A1774
28
FC5
SOFTWARE
ASP B:529 , LEU B:530 , ASP B:531 , ASP B:673 , LEU B:674 , HOH B:2095
BINDING SITE FOR RESIDUE CA B1775
29
FC6
SOFTWARE
HIS B:520 , HIS B:522 , HIS B:684 , HOH B:2079
BINDING SITE FOR RESIDUE CU B1776
30
FC7
SOFTWARE
GLU B:572 , PHE B:663 , ASN B:665 , GLU B:667 , HOH B:2117 , HOH B:2120
BINDING SITE FOR RESIDUE CA B1777
31
FC8
SOFTWARE
GLN A:560 , ARG B:383
BINDING SITE FOR RESIDUE CL B1778
[
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 A/B, )
02: VAR_025027 (H167Y, chain A/B, )
03: VAR_052604 (V171M, chain A/B, )
04: VAR_052605 (H203R, chain A/B, )
05: VAR_012064 (Y317H, chain A/B, )
06: VAR_024343 (R329Q, chain A/B, )
07: VAR_025028 (I371T, chain A/B, )
08: VAR_025029 (A408S, chain A/B, )
09: VAR_025030 (R426H, chain A/B, )
10: VAR_025031 (R441W, chain A/B, )
11: VAR_025032 (A582T, chain A/B, )
12: VAR_025033 (G700S, chain A/B, )
13: VAR_025034 (A749V, chain A/B, )
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
A/B
R
78
Q
02
UniProt
VAR_025027
H
167
Y
AOC3_HUMAN
Polymorphism
2228470
A/B
H
167
Y
03
UniProt
VAR_052604
V
171
M
AOC3_HUMAN
Polymorphism
408038
A/B
V
171
M
04
UniProt
VAR_052605
H
203
R
AOC3_HUMAN
Polymorphism
630079
A/B
H
203
R
05
UniProt
VAR_012064
Y
317
H
AOC3_HUMAN
Polymorphism
438287
A/B
Y
317
H
06
UniProt
VAR_024343
R
329
Q
AOC3_HUMAN
Polymorphism
2229595
A/B
R
329
Q
07
UniProt
VAR_025028
I
371
T
AOC3_HUMAN
Polymorphism
35097308
A/B
I
371
T
08
UniProt
VAR_025029
A
408
S
AOC3_HUMAN
Polymorphism
35643019
A/B
A
408
S
09
UniProt
VAR_025030
R
426
H
AOC3_HUMAN
Polymorphism
33986943
A/B
R
426
H
10
UniProt
VAR_025031
R
441
W
AOC3_HUMAN
Polymorphism
2229596
A/B
R
441
W
11
UniProt
VAR_025032
A
582
T
AOC3_HUMAN
Polymorphism
34987927
A/B
A
582
T
12
UniProt
VAR_025033
G
700
S
AOC3_HUMAN
Polymorphism
477207
A/B
G
700
S
13
UniProt
VAR_025034
A
749
V
AOC3_HUMAN
Polymorphism
34012919
A/B
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 (A:460-473,B:460-473)
2: COPPER_AMINE_OXID_2 (A:679-692,B: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
A:460-473
B:460-473
-
-
2
COPPER_AMINE_OXID_2
PS01165
Copper amine oxidase copper-binding site signature.
AOC3_HUMAN
679-692
2
A:679-692
B:679-692
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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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(
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(
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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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