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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3X40
Asym. Unit
Info
Asym.Unit (458 KB)
Biol.Unit 1 (451 KB)
Biol.Unit 2 (453 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COPPER AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS: PRODUCT SCHIFF-BASE FORM PRODUCED BY ANAEROBIC REDUCTION IN THE PRESENCE OF SODIUM CHLORIDE
Authors
:
T. Okajima, S. Nakanishi, T. Murakawa, M. Kataoka, H. Hayashi, A. Hamag T. Nakai, Y. Kawano, H. Yamaguchi, K. Tanizawa
Date
:
10 Mar 15 (Deposition) - 19 Aug 15 (Release) - 19 Aug 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (2x)
Biol. Unit 2: B (2x)
Keywords
:
Copper Amine Oxidase, Topaquinone, Tpq, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Murakawa, A. Hamaguchi, S. Nakanishi, M. Kataoka, T. Nakai, Y. Kawano, H. Yamaguchi, H. Hayashi, K. Tanizawa, T. Okajima
Probing The Catalytic Mechanism Of Copper Amine Oxidase Fro Arthrobacter Globiformis With Halide Ions
J. Biol. Chem. 2015
[
close entry info
]
Hetero Components
(5, 18)
Info
All Hetero Components
1a: 2-HYDROXY-5-{[(1E)-2-PHENYLETHYLID... (2TYa)
1b: 2-HYDROXY-5-{[(1E)-2-PHENYLETHYLID... (2TYb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: COPPER (II) ION (CUa)
3b: COPPER (II) ION (CUb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2TY
2
Mod. Amino Acid
2-HYDROXY-5-{[(1E)-2-PHENYLETHYLIDENE]AMINO}-L-TYROSINE
2
CL
5
Ligand/Ion
CHLORIDE ION
3
CU
2
Ligand/Ion
COPPER (II) ION
4
GOL
6
Ligand/Ion
GLYCEROL
5
NA
3
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:431 , HIS A:433 , HIS A:592 , CL A:702 , HOH A:1370
BINDING SITE FOR RESIDUE CU A 701
02
AC2
SOFTWARE
2TY A:382 , HIS A:431 , HIS A:433 , HIS A:592 , MET A:602 , CU A:701 , HOH A:824 , HOH A:1370
BINDING SITE FOR RESIDUE CL A 702
03
AC3
SOFTWARE
HIS A:345 , SER A:374 , TYR A:387 , HOH A:1150 , HOH A:1347
BINDING SITE FOR RESIDUE CL A 703
04
AC4
SOFTWARE
ALA A:93 , ALA A:94 , ARG A:148 , SER A:562 , VAL B:79 , THR B:80
BINDING SITE FOR RESIDUE NA A 704
05
AC5
SOFTWARE
ARG A:49 , ASP A:440 , MET A:441 , PHE A:446 , ASP A:581 , ILE A:582 , HOH A:831
BINDING SITE FOR RESIDUE NA A 705
06
AC6
SOFTWARE
GLU A:347 , ARG A:370 , LYS A:401 , GOL A:710 , HOH A:852 , HOH A:998 , HOH A:1020 , HOH A:1334
BINDING SITE FOR RESIDUE GOL A 706
07
AC7
SOFTWARE
HIS A:515 , ASP A:605 , LYS A:610 , HOH A:1243 , HOH A:1266 , HOH A:1340
BINDING SITE FOR RESIDUE GOL A 707
08
AC8
SOFTWARE
ASP A:161 , HIS A:170 , VAL A:197 , ALA A:199 , HOH B:1265
BINDING SITE FOR RESIDUE GOL A 708
09
AC9
SOFTWARE
ILE A:39 , ALA A:40 , TYR A:41 , LEU A:42 , VAL A:251 , ILE A:328 , SER A:329 , ASP A:330 , HOH A:912 , HOH A:982
BINDING SITE FOR RESIDUE GOL A 709
10
BC1
SOFTWARE
TRP A:349 , ARG A:370 , TYR A:389 , GLU A:397 , GLU A:399 , GOL A:706 , HOH A:1334
BINDING SITE FOR RESIDUE GOL A 710
11
BC2
SOFTWARE
HIS B:431 , HIS B:433 , HIS B:592 , CL B:702 , HOH B:1319
BINDING SITE FOR RESIDUE CU B 701
12
BC3
SOFTWARE
2TY B:382 , HIS B:431 , HIS B:433 , HIS B:592 , MET B:602 , CU B:701 , HOH B:1309 , HOH B:1319
BINDING SITE FOR RESIDUE CL B 702
13
BC4
SOFTWARE
HIS B:345 , SER B:374 , TYR B:387 , HOH B:1204
BINDING SITE FOR RESIDUE CL B 703
14
BC5
SOFTWARE
ASP B:128
BINDING SITE FOR RESIDUE CL B 704
15
BC6
SOFTWARE
ASP B:440 , MET B:441 , ASP B:581 , ILE B:582 , HOH B:885
BINDING SITE FOR RESIDUE NA B 705
16
BC7
SOFTWARE
GLU B:347 , ASP B:348 , TRP B:349 , ARG B:370 , LYS B:401 , HOH B:859 , HOH B:1076
BINDING SITE FOR RESIDUE GOL B 706
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
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
[
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 (458 KB)
Header - Asym.Unit
Biol.Unit 1 (451 KB)
Header - Biol.Unit 1
Biol.Unit 2 (453 KB)
Header - Biol.Unit 2
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
3X40
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
