PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1PU4
Asym. Unit
Info
Asym.Unit (234 KB)
Biol.Unit 1 (225 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN VASCULAR ADHESION PROTEIN-1
Authors
:
T. A. Salminen, T. T. Airenne
Date
:
24 Jun 03 (Deposition) - 03 May 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Amine Oxidase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. T. Airenne, Y. Nymalm, H. Kidron, D. J. Smith, M. Pihlavisto, M. Salmi, S. Jalkanen, M. S. Johnson, T. A. Salminen
Crystal Structure Of The Human Vascular Adhesion Protein-1: Unique Structural Features With Functional Implications.
Protein Sci. V. 14 1964 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 14)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
4b: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CU
2
Ligand/Ion
COPPER (II) ION
3
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
TPQ
2
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:130 , GLN A:133 , ASN A:137 , NAG A:2780
BINDING SITE FOR RESIDUE NAG A 2779
02
AC2
SOFTWARE
NAG A:2779
BINDING SITE FOR RESIDUE NAG A 2780
03
AC3
SOFTWARE
ARG A:206 , ASN A:232 , SER A:234 , TYR B:448 , SER B:449
BINDING SITE FOR RESIDUE NAG A 2781
04
AC4
SOFTWARE
PHE B:130 , GLN B:133 , ASN B:137 , NAG B:2780
BINDING SITE FOR RESIDUE NAG B 2779
05
AC5
SOFTWARE
NAG B:2779
BINDING SITE FOR RESIDUE NAG B 2780
06
AC6
SOFTWARE
ASN B:232 , SER B:234
BINDING SITE FOR RESIDUE NAG B 2781
07
AC7
SOFTWARE
TPQ A:471 , HIS A:520 , HIS A:522 , HIS A:684
BINDING SITE FOR RESIDUE CU A 801
08
AC8
SOFTWARE
LYS A:106 , ASP A:529 , LEU A:530 , ASP A:531 , ASP A:673 , LEU A:674
BINDING SITE FOR RESIDUE CA A 802
09
AC9
SOFTWARE
GLU A:572 , LYS A:638 , GLU A:641 , PHE A:663 , ASN A:665 , GLU A:667
BINDING SITE FOR RESIDUE CA A 803
10
BC1
SOFTWARE
TPQ B:471 , HIS B:520 , HIS B:522 , HIS B:684
BINDING SITE FOR RESIDUE CU B 801
11
BC2
SOFTWARE
LYS B:106 , ASP B:529 , LEU B:530 , ASP B:531 , ASN B:537 , ASP B:673 , LEU B:674
BINDING SITE FOR RESIDUE CA B 802
12
BC3
SOFTWARE
GLU B:572 , LYS B:638 , GLU B:641 , PHE B:663 , ASN B:665 , GLU B:667
BINDING SITE FOR RESIDUE CA B 803
[
close Site info
]
SAPs(SNPs)/Variants
(12, 24)
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_012064 (Y317H, chain A/B, )
05: VAR_024343 (R329Q, chain A/B, )
06: VAR_025028 (I371T, chain A/B, )
07: VAR_025029 (A408S, chain A/B, )
08: VAR_025030 (R426H, chain A/B, )
09: VAR_025031 (R441W, chain A/B, )
10: VAR_025032 (A582T, chain A/B, )
11: VAR_025033 (G700S, chain A/B, )
12: 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_012064
Y
317
H
AOC3_HUMAN
Polymorphism
438287
A/B
Y
317
H
05
UniProt
VAR_024343
R
329
Q
AOC3_HUMAN
Polymorphism
2229595
A/B
R
329
Q
06
UniProt
VAR_025028
I
371
T
AOC3_HUMAN
Polymorphism
35097308
A/B
I
371
T
07
UniProt
VAR_025029
A
408
S
AOC3_HUMAN
Polymorphism
35643019
A/B
A
408
S
08
UniProt
VAR_025030
R
426
H
AOC3_HUMAN
Polymorphism
33986943
A/B
R
426
H
09
UniProt
VAR_025031
R
441
W
AOC3_HUMAN
Polymorphism
2229596
A/B
R
441
W
10
UniProt
VAR_025032
A
582
T
AOC3_HUMAN
Polymorphism
34987927
A/B
A
582
T
11
UniProt
VAR_025033
G
700
S
AOC3_HUMAN
Polymorphism
477207
A/B
G
700
S
12
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:55-534 (gaps) | B:57-534 (gaps))
Exon 1.2 (A:534-629 | B:534-629)
Exon 1.3 (A:629-672 | B:629-672)
Exon 1.4 (A:673-761 | B:673-761 (gaps))
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:55-534 (gaps)
B:57-534 (gaps)
480
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:673-761
B:673-761 (gaps)
89
89
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1pu4A01 (A:55-165)
1b: CATH_1pu4B01 (B:57-165)
1c: CATH_1pu4A02 (A:166-297)
1d: CATH_1pu4B02 (B:166-297)
2a: CATH_1pu4B03 (B:322-741)
2b: CATH_1pu4A03 (A:322-728)
View:
Select:
Label:
Classes
(
)
(
)
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
1pu4A01
A:55-165
1b
1pu4B01
B:57-165
1c
1pu4A02
A:166-297
1d
1pu4B02
B:166-297
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
1pu4B03
B:322-741
2b
1pu4A03
A:322-728
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cu_amine_oxidN2_1pu4B01 (B:66-152)
1b: PFAM_Cu_amine_oxidN2_1pu4B02 (B:66-152)
2a: PFAM_Cu_amine_oxidN3_1pu4B03 (B:169-269)
2b: PFAM_Cu_amine_oxidN3_1pu4B04 (B:169-269)
3a: PFAM_Cu_amine_oxid_1pu4B05 (B:313-724)
3b: PFAM_Cu_amine_oxid_1pu4B06 (B:313-724)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CuAO_N2_N3
(40)
Family
:
Cu_amine_oxidN2
(27)
Homo sapiens (Human)
(3)
1a
Cu_amine_oxidN2-1pu4B01
B:66-152
1b
Cu_amine_oxidN2-1pu4B02
B:66-152
Family
:
Cu_amine_oxidN3
(37)
Homo sapiens (Human)
(3)
2a
Cu_amine_oxidN3-1pu4B03
B:169-269
2b
Cu_amine_oxidN3-1pu4B04
B:169-269
Clan
:
no clan defined [family: Cu_amine_oxid]
(40)
Family
:
Cu_amine_oxid
(40)
Homo sapiens (Human)
(3)
3a
Cu_amine_oxid-1pu4B05
B:313-724
3b
Cu_amine_oxid-1pu4B06
B:313-724
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (234 KB)
Header - Asym.Unit
Biol.Unit 1 (225 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1PU4
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help