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.
1VAY
Asym. Unit
Info
Asym.Unit (393 KB)
Biol.Unit 1 (197 KB)
Biol.Unit 2 (197 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 URICASE FROM ARTHROBACTER GLOBIFORMIS WITH INHIBITOR 8-AZAXANTHINE
Authors
:
M. T. Hossain, K. Suzuki, T. Yamamoto, S. Imamura, T. Sekiguchi, A. Takenaka
Date
:
19 Feb 04 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.24
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. T. Hossain, E. C. M. Juan, K. Suzuki, T. Yamamoto, S. Imamura, T. Sekiguchi, A. Takenaka
Crystal Structure Of Uricase From Arthrobacter Globiformis Complexed With An Inhibitor 8-Azaxanthine
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: 8-AZAXANTHINE (AZAa)
1b: 8-AZAXANTHINE (AZAb)
1c: 8-AZAXANTHINE (AZAc)
1d: 8-AZAXANTHINE (AZAd)
1e: 8-AZAXANTHINE (AZAe)
1f: 8-AZAXANTHINE (AZAf)
1g: 8-AZAXANTHINE (AZAg)
1h: 8-AZAXANTHINE (AZAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZA
8
Ligand/Ion
8-AZAXANTHINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE B:163 , ARG B:180 , LEU B:222 , GLN B:223 , ASN B:249 , HOH B:1388 , TYR C:20 , VAL C:64 , THR C:67 , HOH C:349
BINDING SITE FOR RESIDUE AZA B 1301
2
AC2
SOFTWARE
TYR A:20 , VAL A:64 , ALA A:66 , THR A:67 , PHE D:163 , LEU D:174 , ARG D:180 , LEU D:222 , GLN D:223 , ASN D:249 , HOH D:1335
BINDING SITE FOR RESIDUE AZA D 1302
3
AC3
SOFTWARE
TYR B:20 , VAL B:64 , ALA B:66 , THR B:67 , HOH B:1373 , PHE C:163 , ARG C:180 , ALA C:221 , LEU C:222 , GLN C:223 , ASN C:249
BINDING SITE FOR RESIDUE AZA B 1303
4
AC4
SOFTWARE
PHE A:163 , LEU A:174 , ARG A:180 , ALA A:221 , LEU A:222 , GLN A:223 , HOH A:1425 , TYR D:20 , VAL D:64 , ALA D:66 , THR D:67
BINDING SITE FOR RESIDUE AZA A 1304
5
AC5
SOFTWARE
TYR E:20 , VAL E:64 , THR E:67 , PHE H:163 , LEU H:174 , ARG H:180 , ALA H:221 , LEU H:222 , GLN H:223 , ASN H:249
BINDING SITE FOR RESIDUE AZA H 1305
6
AC6
SOFTWARE
VAL F:64 , ALA F:66 , THR F:67 , PHE G:163 , LEU G:174 , ARG G:180 , ALA G:221 , LEU G:222 , GLN G:223 , ASN G:249 , HOH G:1428
BINDING SITE FOR RESIDUE AZA G 1306
7
AC7
SOFTWARE
PHE F:163 , ARG F:180 , ALA F:221 , LEU F:222 , GLN F:223 , ASN F:249 , HOH F:1418 , TYR G:20 , VAL G:64 , ALA G:66 , THR G:67
BINDING SITE FOR RESIDUE AZA F 1307
8
AC8
SOFTWARE
PHE E:163 , LEU E:174 , ARG E:180 , ALA E:221 , LEU E:222 , GLN E:223 , ASN E:249 , HOH E:1374 , TYR H:20 , VAL H:64 , THR H:67 , HOH H:1339
BINDING SITE FOR RESIDUE AZA E 1308
[
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
(1, 16)
Info
All SCOP Domains
1a: SCOP_d1vaya1 (A:142-297)
1b: SCOP_d1vaya2 (A:11-141)
1c: SCOP_d1vayb1 (B:142-297)
1d: SCOP_d1vayb2 (B:11-141)
1e: SCOP_d1vayc1 (C:142-297)
1f: SCOP_d1vayc2 (C:11-141)
1g: SCOP_d1vayd1 (D:142-297)
1h: SCOP_d1vayd2 (D:11-141)
1i: SCOP_d1vaye1 (E:142-297)
1j: SCOP_d1vaye2 (E:11-141)
1k: SCOP_d1vayf1 (F:142-297)
1l: SCOP_d1vayf2 (F:11-141)
1m: SCOP_d1vayg1 (G:142-297)
1n: SCOP_d1vayg2 (G:11-141)
1o: SCOP_d1vayh1 (H:142-297)
1p: SCOP_d1vayh2 (H:11-141)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
T-fold
(116)
Superfamily
:
Tetrahydrobiopterin biosynthesis enzymes-like
(113)
Family
:
Urate oxidase (uricase)
(60)
Protein domain
:
Urate oxidase (uricase)
(56)
Arthrobacter globiformis [TaxId: 1665]
(2)
1a
d1vaya1
A:142-297
1b
d1vaya2
A:11-141
1c
d1vayb1
B:142-297
1d
d1vayb2
B:11-141
1e
d1vayc1
C:142-297
1f
d1vayc2
C:11-141
1g
d1vayd1
D:142-297
1h
d1vayd2
D:11-141
1i
d1vaye1
E:142-297
1j
d1vaye2
E:11-141
1k
d1vayf1
F:142-297
1l
d1vayf2
F:11-141
1m
d1vayg1
G:142-297
1n
d1vayg2
G:11-141
1o
d1vayh1
H:142-297
1p
d1vayh2
H:11-141
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1vayA00 (A:11-297)
1b: CATH_1vayC00 (C:11-297)
1c: CATH_1vayD00 (D:11-297)
1d: CATH_1vayE00 (E:11-297)
1e: CATH_1vayF00 (F:11-297)
1f: CATH_1vayG00 (G:11-297)
1g: CATH_1vayH00 (H:11-297)
1h: CATH_1vayB00 (B:11-297)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Urate Oxidase
(38)
Homologous Superfamily
:
Urate Oxidase;
(38)
Arthrobacter globiformis. Organism_taxid: 1665
(2)
1a
1vayA00
A:11-297
1b
1vayC00
C:11-297
1c
1vayD00
D:11-297
1d
1vayE00
E:11-297
1e
1vayF00
F:11-297
1f
1vayG00
G:11-297
1g
1vayH00
H:11-297
1h
1vayB00
B:11-297
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
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 (393 KB)
Header - Asym.Unit
Biol.Unit 1 (197 KB)
Header - Biol.Unit 1
Biol.Unit 2 (197 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
1VAY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
