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2C11
Biol. Unit 2
Info
Asym.Unit (455 KB)
Biol.Unit 1 (224 KB)
Biol.Unit 2 (225 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE 2-HYDRAZINOPYRIDINE OF SEMICARBAZIDE-SENSITIVE AMINE OXIDASE
Authors
:
E. Jakobsson, G. J. Kleywegt
Date
:
09 Sep 05 (Deposition) - 20 Sep 06 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Oxidoreductase, Adhesion Protein-1, 2-Hydroxypyridine, Metal-Binding, Cell Adhesion, Glycoprotein, 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
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Hetero Components
(6, 20)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
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)
4a: COPPER (II) ION (CUa)
4aa: COPPER (II) ION (CUaa)
4ab: COPPER (II) ION (CUab)
4ac: COPPER (II) ION (CUac)
4ad: COPPER (II) ION (CUad)
4b: COPPER (II) ION (CUb)
4c: COPPER (II) ION (CUc)
4d: COPPER (II) ION (CUd)
4e: COPPER (II) ION (CUe)
4f: COPPER (II) ION (CUf)
4g: COPPER (II) ION (CUg)
4h: COPPER (II) ION (CUh)
4i: COPPER (II) ION (CUi)
4j: COPPER (II) ION (CUj)
4k: COPPER (II) ION (CUk)
4l: COPPER (II) ION (CUl)
4m: COPPER (II) ION (CUm)
4n: COPPER (II) ION (CUn)
4o: COPPER (II) ION (CUo)
4p: COPPER (II) ION (CUp)
4q: COPPER (II) ION (CUq)
4r: COPPER (II) ION (CUr)
4s: COPPER (II) ION (CUs)
4t: COPPER (II) ION (CUt)
4u: COPPER (II) ION (CUu)
4v: COPPER (II) ION (CUv)
4w: COPPER (II) ION (CUw)
4x: COPPER (II) ION (CUx)
4y: COPPER (II) ION (CUy)
4z: COPPER (II) ION (CUz)
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)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
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)
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)
9a: 2-OXY-4-HYDROXY-5-(2-HYDRAZINOPYRI... (PAQa)
9b: 2-OXY-4-HYDROXY-5-(2-HYDRAZINOPYRI... (PAQb)
9c: 2-OXY-4-HYDROXY-5-(2-HYDRAZINOPYRI... (PAQc)
9d: 2-OXY-4-HYDROXY-5-(2-HYDRAZINOPYRI... (PAQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
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
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
9
PAQ
2
Mod. Amino Acid
2-OXY-4-HYDROXY-5-(2-HYDRAZINOPYRIDINE)PHENYLALANINE
[
close Hetero Component info
]
Sites
(30, 30)
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: FC7 (SOFTWARE)
23: FC8 (SOFTWARE)
24: FC9 (SOFTWARE)
25: GC1 (SOFTWARE)
26: GC2 (SOFTWARE)
27: GC3 (SOFTWARE)
28: GC4 (SOFTWARE)
29: GC5 (SOFTWARE)
30: GC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC4
SOFTWARE
ASP C:529 , LEU C:530 , ASP C:531 , ASP C:673 , LEU C:674
BINDING SITE FOR RESIDUE CA C1737
02
CC5
SOFTWARE
PAQ C:471 , HIS C:520 , HIS C:522 , HIS C:684
BINDING SITE FOR RESIDUE CU C1738
03
CC6
SOFTWARE
GLU C:572 , LYS C:638 , PHE C:663 , ASN C:665 , GLU C:667
BINDING SITE FOR RESIDUE CA C1739
04
CC7
SOFTWARE
ARG C:383 , GLN D:560
BINDING SITE FOR RESIDUE CL C1740
05
CC8
SOFTWARE
HIS C:112
BINDING SITE FOR RESIDUE CU C1741
06
CC9
SOFTWARE
GLU C:140 , HIS C:160
BINDING SITE FOR RESIDUE CU C1742
07
DC1
SOFTWARE
HIS C:167
BINDING SITE FOR RESIDUE CU C1743
08
DC2
SOFTWARE
HIS C:414
BINDING SITE FOR RESIDUE CU C1744
09
DC3
SOFTWARE
HIS C:444 , ASP C:446
BINDING SITE FOR RESIDUE CU C1745
10
DC4
SOFTWARE
HIS C:593
BINDING SITE FOR RESIDUE CU C1746
11
DC5
SOFTWARE
HIS C:687 , ARG D:706
BINDING SITE FOR RESIDUE CU C1747
12
DC6
SOFTWARE
LYS D:106 , ASP D:529 , LEU D:530 , ASP D:531 , ASP D:673 , LEU D:674
BINDING SITE FOR RESIDUE CA D1741
13
DC7
SOFTWARE
PAQ D:471 , HIS D:520 , HIS D:522 , HIS D:684
BINDING SITE FOR RESIDUE CU D1742
14
DC8
SOFTWARE
GLU D:572 , PHE D:663 , ASN D:665 , GLU D:667
BINDING SITE FOR RESIDUE CA D1743
15
DC9
SOFTWARE
LEU C:559 , GLN C:560 , ARG D:383
BINDING SITE FOR RESIDUE CL D1744
16
EC1
SOFTWARE
HIS D:112
BINDING SITE FOR RESIDUE CU D1745
17
EC2
SOFTWARE
GLU D:140 , HIS D:160 , SER D:646 , PHE D:648
BINDING SITE FOR RESIDUE CU D1746
18
EC3
SOFTWARE
PRO D:165 , HIS D:167
BINDING SITE FOR RESIDUE CU D1747
19
EC4
SOFTWARE
ASP D:412 , HIS D:414
BINDING SITE FOR RESIDUE CU D1748
20
EC5
SOFTWARE
HIS D:444 , ASP D:446 , GLY D:727
BINDING SITE FOR RESIDUE CU D1749
21
EC6
SOFTWARE
HIS D:687 , ASP D:690
BINDING SITE FOR RESIDUE CU D1750
22
FC7
SOFTWARE
PHE C:130 , GLN C:133 , ASN C:137
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 137 RESIDUES 1730 TO 1731
23
FC8
SOFTWARE
VAL C:209 , ASN C:232 , SER C:234 , TYR D:448
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 232 RESIDUES 1735 TO 1735
24
FC9
SOFTWARE
ASN C:294
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 294 RESIDUES 1736 TO 1736
25
GC1
SOFTWARE
GLU C:282 , ASN C:592 , HIS C:593 , GLY C:671
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 592 RESIDUES 1732 TO 1734
26
GC2
SOFTWARE
SER C:449 , PHE D:130 , GLN D:133 , ASN D:137 , MET D:152 , VAL D:157 , PRO D:163 , ARG D:206 , ASN D:232 , SER D:234 , GLU D:282 , ASN D:294 , GLU D:536 , ASN D:592 , GLY D:671 , BMA D:1739
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 137 RESIDUES 1730 TO 1737
27
GC3
SOFTWARE
SER C:449 , ARG D:206 , ASN D:232 , SER D:234
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 232 RESIDUES 1735 TO 1735
28
GC4
SOFTWARE
ASN D:294
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 294 RESIDUES 1736 TO 1736
29
GC5
SOFTWARE
SER C:449 , HIS D:203 , ARG D:206 , ASN D:232 , SER D:234 , GLU D:282 , ASN D:294 , GLU D:536 , ASN D:592 , ASN D:666 , GLY D:671 , NAG D:1731
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 592 RESIDUES 1732 TO 1740
30
GC6
SOFTWARE
ASN D:666
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 666 RESIDUES 1738 TO 1738
[
close Site info
]
SAPs(SNPs)/Variants
(12, 24)
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, )
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
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
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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:
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Label:
Sorry, no Info available
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2c11A01 (A:58-171)
1b: CATH_2c11B01 (B:58-171)
1c: CATH_2c11C01 (C:58-171)
1d: CATH_2c11D01 (D:58-171)
1e: CATH_2c11A02 (A:172-307)
1f: CATH_2c11B02 (B:172-307)
1g: CATH_2c11C02 (C:172-307)
1h: CATH_2c11D02 (D:172-307)
2a: CATH_2c11A03 (A:308-729)
2b: CATH_2c11B03 (B:308-729)
2c: CATH_2c11C03 (C:308-729)
2d: CATH_2c11D03 (D:308-729)
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Classes
(
)
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Architectures
(
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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
2c11A01
A:58-171
1b
2c11B01
B:58-171
1c
2c11C01
C:58-171
1d
2c11D01
D:58-171
1e
2c11A02
A:172-307
1f
2c11B02
B:172-307
1g
2c11C02
C:172-307
1h
2c11D02
D:172-307
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
2c11A03
A:308-729
2b
2c11B03
B:308-729
2c
2c11C03
C:308-729
2d
2c11D03
D:308-729
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain D
Asymmetric Unit 1
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