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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'Exon' information from database.
4BTY
Asym. Unit
Info
Asym.Unit (246 KB)
Biol.Unit 1 (236 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN VASCULAR ADHESION PROTEIN-1 IN COMPLEX WITH PYRIDAZINONE INHIBITORS
Authors
:
E. Bligt-Linden, M. Pihlavisto, I. Szatmari, Z. Otwinowski, D. J. Smit L. Lazar, F. Fulop, T. A. Salminen
Date
:
19 Jun 13 (Deposition) - 18 Dec 13 (Release) - 15 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Bligt-Linden, M. Pihlavisto, I. Szatmari, Z. Otwinowski, D. J. Smith, L. Lazar, F. Fulop, T. A. Salminen
Novel Pyridazinone Inhibitors For Vascular Adhesion Protein- 1 (Vap-1): Old Target - New Inhibition Mode.
J. Med. Chem. V. 56 9837 2013
[
close entry info
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Hetero Components
(7, 25)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: COPPER (II) ION (CUa)
3b: COPPER (II) ION (CUb)
4a: 5-[4-(4-METHYLPIPERAZIN-1-YL)PHENY... (JWFa)
4b: 5-[4-(4-METHYLPIPERAZIN-1-YL)PHENY... (JWFb)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
7a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
7b: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
4
Ligand/Ion
CALCIUM ION
3
CU
2
Ligand/Ion
COPPER (II) ION
4
JWF
2
Ligand/Ion
5-[4-(4-METHYLPIPERAZIN-1-YL)PHENYLAMINO]-2-(4-CHLOROPHENYL)-6-(1H-1,2,4-TRIAZOL-5-YL)-3(2H)-PYRIDAZINONE
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
TPQ
2
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:520 , HIS A:522 , HIS A:684
BINDING SITE FOR RESIDUE CU A1762
02
AC2
SOFTWARE
ASP A:529 , LEU A:530 , ASP A:531 , ASP A:673 , LEU A:674
BINDING SITE FOR RESIDUE CA A1763
03
AC3
SOFTWARE
GLU A:572 , GLU A:641 , PHE A:663 , ASN A:665 , GLU A:667
BINDING SITE FOR RESIDUE CA A1764
04
AC4
SOFTWARE
PHE A:173 , TYR A:176 , LEU A:177 , ASP A:180 , PHE A:227 , PHE A:389 , TYR A:394 , LEU A:469 , HIS A:762 , TYR B:448
BINDING SITE FOR RESIDUE JWF A2000
05
AC5
SOFTWARE
HIS B:520 , HIS B:522 , HIS B:684 , HOH B:2008
BINDING SITE FOR RESIDUE CU B1762
06
AC6
SOFTWARE
ASP B:529 , LEU B:530 , ASP B:531 , ASP B:673 , LEU B:674
BINDING SITE FOR RESIDUE CA B1763
07
AC7
SOFTWARE
GLU B:572 , LYS B:638 , GLU B:641 , PHE B:663 , ASN B:665 , GLU B:667
BINDING SITE FOR RESIDUE CA B1764
08
AC8
SOFTWARE
ASN B:592 , HIS B:593
BINDING SITE FOR RESIDUE NAG B1772
09
AC9
SOFTWARE
TYR A:448 , PHE B:173 , LEU B:177 , ASP B:180 , THR B:210 , THR B:212 , PHE B:389 , TYR B:394 , LEU B:469 , HIS B:762 , HOH B:2002
BINDING SITE FOR RESIDUE JWF B2000
10
BC1
SOFTWARE
PHE A:130 , GLN A:133 , ASN A:137 , SER A:139
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1765 THROUGH NAG A1766 BOUND TO ASN A 137
11
BC2
SOFTWARE
ARG A:206 , ASN A:232 , SER A:234
BINDING SITE FOR MONO-SACCHARIDE NAG A1767 BOUND TO ASN A 232
12
BC3
SOFTWARE
ASN A:294
BINDING SITE FOR MONO-SACCHARIDE NAG A1768 BOUND TO ASN A 294
13
BC4
SOFTWARE
ASN A:592
BINDING SITE FOR MONO-SACCHARIDE NAG A1769 BOUND TO ASN A 592
14
BC5
SOFTWARE
ASN A:666
BINDING SITE FOR MONO-SACCHARIDE NAG A1770 BOUND TO ASN A 666
15
BC6
SOFTWARE
PHE B:130 , GLN B:133 , ASN B:137 , PRO B:163
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1765 THROUGH MAN B1769 BOUND TO ASN B 137
16
BC7
SOFTWARE
SER A:449 , ASP A:728 , ASN B:232 , SER B:234
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1770 THROUGH NAG B1771 BOUND TO ASN B 232
17
BC8
SOFTWARE
ASN B:666
BINDING SITE FOR MONO-SACCHARIDE NAG B1773 BOUND TO ASN B 666
[
close Site info
]
SAPs(SNPs)/Variants
(13, 26)
Info
(mutated residues are not available)
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
(4, 8)
Info
All Exons
Exon 1.1 (A:53-534 | B:57-534)
Exon 1.2 (A:534-629 | B:534-629)
Exon 1.3 (A:629-672 | B:629-672)
Exon 1.4 (A:673-763 | B:673-763)
View:
Select:
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/-
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
ENST00000308423
1
ENSE00001213814
chr17:
41003201-41004960
1760
AOC3_HUMAN
1-534
534
2
A:53-534
B:57-534
482
478
1.2
ENST00000308423
2
ENSE00000899074
chr17:
41006465-41006750
286
AOC3_HUMAN
534-629
96
2
A:534-629
B:534-629
96
96
1.3
ENST00000308423
3
ENSE00001213800
chr17:
41007461-41007590
130
AOC3_HUMAN
629-672
44
2
A:629-672
B:629-672
44
44
1.4
ENST00000308423
4
ENSE00001178316
chr17:
41008292-41010138
1847
AOC3_HUMAN
673-763
91
2
A:673-763
B:673-763
91
91
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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Asym.Unit (246 KB)
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