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.
1SXS
Asym. Unit
Info
Asym.Unit (57 KB)
Biol.Unit 1 (52 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
REDUCED BOVINE SUPEROXIDE DISMUTASE AT PH 5.0 COMPLEXED WITH THIOCYANATE
Authors
:
M. Ferraroni, W. R. Rypniewski, B. Bruni, P. Orioli, S. Mangani
Date
:
24 Sep 98 (Deposition) - 30 Sep 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, Superoxide Acceptor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Ferraroni, W. R. Rypniewski, B. Bruni, P. Orioli, S. Mangani
Crystallographic Determination Of Reduced Bovine Superoxide Dismutase At Ph 5. 0 And Of Anion Binding To Its Active Site
J. Biol. Inorg. Chem. V. 3 411 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
3a: THIOCYANATE ION (SCNa)
3b: THIOCYANATE ION (SCNb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CU
2
Ligand/Ion
COPPER (II) ION
3
SCN
2
Ligand/Ion
THIOCYANATE ION
4
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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: MA (AUTHOR)
10: MB (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:46 , PRO A:60 , HIS A:61 , HIS A:118 , THR A:135 , ARG A:141 , CU A:152 , HOH A:162 , HOH A:163 , HOH A:251
BINDING SITE FOR RESIDUE SCN A 155
02
AC2
SOFTWARE
HIS B:44 , HIS B:46 , HIS B:61 , HIS B:118 , THR B:135 , ARG B:141 , CU B:152 , HOH B:193 , HOH B:195
BINDING SITE FOR RESIDUE SCN B 155
03
AC3
SOFTWARE
HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118 , SCN A:155
BINDING SITE FOR RESIDUE CU A 152
04
AC4
SOFTWARE
HIS A:61 , HIS A:69 , HIS A:78 , ASP A:81
BINDING SITE FOR RESIDUE ZN A 153
05
AC5
SOFTWARE
HIS B:44 , HIS B:46 , HIS B:61 , HIS B:118 , SCN B:155
BINDING SITE FOR RESIDUE CU B 152
06
AC6
SOFTWARE
HIS B:61 , HIS B:69 , HIS B:78 , ASP B:81
BINDING SITE FOR RESIDUE ZN B 153
07
AC7
SOFTWARE
GLU A:119 , GLY A:139 , SER A:140 , HOH A:188
BINDING SITE FOR RESIDUE CA A 154
08
AC8
SOFTWARE
GLU B:119 , GLY B:139 , SER B:140
BINDING SITE FOR RESIDUE CA B 154
09
MA
AUTHOR
HIS A:44 , HIS A:46 , HIS A:61 , HIS A:69 , HIS A:78 , ASP A:81 , HIS A:118 , CU A:152 , ZN A:153
METAL BINDING SITE
10
MB
AUTHOR
HIS B:44 , HIS B:46 , HIS B:61 , HIS B:69 , HIS B:78 , ASP B:81 , HIS B:118 , CU B:152 , ZN B:153
METAL BINDING SITE
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: SOD_CU_ZN_1 (A:42-52,B:42-52)
2: SOD_CU_ZN_2 (A:136-147,B:136-147)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SOD_CU_ZN_1
PS00087
Copper/Zinc superoxide dismutase signature 1.
SODC_BOVIN
43-53
2
A:42-52
B:42-52
2
SOD_CU_ZN_2
PS00332
Copper/Zinc superoxide dismutase signature 2.
SODC_BOVIN
137-148
2
A:136-147
B:136-147
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.1 (A:1-23 | B:1-23)
Exon 1.2 (A:24-54 | B:24-54)
Exon 1.3 (A:54-77 | B:54-77)
Exon 1.4 (A:77-116 | B:77-116)
Exon 1.5 (A:117-151 | B:117-151)
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 1.4/1.5
6: Boundary 1.5/-
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
ENSBTAT00000032452
1
ENSBTAE00000259570
chr1:
2920927-2920763
165
SODC_BOVIN
1-24
24
2
A:1-23
B:1-23
23
23
1.2
ENSBTAT00000032452
2
ENSBTAE00000204052
chr1:
2917164-2917074
91
SODC_BOVIN
25-55
31
2
A:24-54
B:24-54
31
31
1.3
ENSBTAT00000032452
3
ENSBTAE00000204053
chr1:
2915376-2915307
70
SODC_BOVIN
55-78
24
2
A:54-77
B:54-77
24
24
1.4
ENSBTAT00000032452
4
ENSBTAE00000204054
chr1:
2914479-2914362
118
SODC_BOVIN
78-117
40
2
A:77-116
B:77-116
40
40
1.5
ENSBTAT00000032452
5
ENSBTAE00000204055
chr1:
2912760-2912336
425
SODC_BOVIN
118-152
35
2
A:117-151
B:117-151
35
35
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1sxsa_ (A:)
1b: SCOP_d1sxsb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Cu,Zn superoxide dismutase-like
(165)
Family
:
Cu,Zn superoxide dismutase-like
(158)
Protein domain
:
Cu,Zn superoxide dismutase, SOD
(134)
Cow (Bos taurus) [TaxId: 9913]
(23)
1a
d1sxsa_
A:
1b
d1sxsb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1sxsA00 (A:1-151)
1b: CATH_1sxsB00 (B:1-151)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.200, no name defined]
(125)
Cattle (Bos taurus)
(14)
1a
1sxsA00
A:1-151
1b
1sxsB00
B:1-151
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Sod_Cu_1sxsB01 (B:4-147)
1b: PFAM_Sod_Cu_1sxsB02 (B:4-147)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sod_Cu]
(71)
Family
:
Sod_Cu
(71)
Bos taurus (Bovine)
(12)
1a
Sod_Cu-1sxsB01
B:4-147
1b
Sod_Cu-1sxsB02
B:4-147
[
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 (57 KB)
Header - Asym.Unit
Biol.Unit 1 (52 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
1SXS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
