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.
1YAI
Biol. Unit 2
Info
Asym.Unit (80 KB)
Biol.Unit 1 (51 KB)
Biol.Unit 2 (51 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE
Authors
:
Y. Bourne, S. M. Redford, T. P. Lo, J. A. Tainer, E. D. Getzoff
Date
:
03 Feb 96 (Deposition) - 20 Aug 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (2x)
Biol. Unit 2: B,C (1x)
Keywords
:
Oxidoreductase, Beta-Barrel, Metalloenzyme, Macromolecular Assembly
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Bourne, S. M. Redford, H. M. Steinman, J. R. Lepock, J. A. Tainer, E. D. Getzoff
Novel Dimeric Interface And Electrostatic Recognition In Bacterial Cu, Zn Superoxide Dismutase.
Proc. Natl. Acad. Sci. Usa V. 93 12774 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(8, 8)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: CU2 (UNKNOWN)
6: CU3 (UNKNOWN)
7: ZN2 (UNKNOWN)
8: ZN3 (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
HIS B:45 , HIS B:47 , HIS B:70 , HIS B:125
BINDING SITE FOR RESIDUE CU B 152
2
AC4
SOFTWARE
HIS B:70 , HIS B:79 , HIS B:88 , ASP B:91
BINDING SITE FOR RESIDUE ZN B 153
3
AC5
SOFTWARE
HIS C:45 , HIS C:47 , HIS C:70 , HIS C:125 , HOH C:154
BINDING SITE FOR RESIDUE CU C 152
4
AC6
SOFTWARE
HIS C:70 , HIS C:79 , HIS C:88 , ASP C:91
BINDING SITE FOR RESIDUE ZN C 153
5
CU2
UNKNOWN
HIS B:45 , HIS B:47 , HIS B:70 , HIS B:125
COPPER BINDING SITE.
6
CU3
UNKNOWN
HIS C:45 , HIS C:47 , HIS C:70 , HIS C:125
COPPER BINDING SITE.
7
ZN2
UNKNOWN
HIS B:70 , HIS B:79 , HIS B:88 , ASP B:91
ZINC BINDING SITE.
8
ZN3
UNKNOWN
HIS C:70 , HIS C:79 , HIS C:88 , ASP C:91
ZINC BINDING SITE.
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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 (B:43-53,C:43-53)
2: SOD_CU_ZN_2 (B:139-150,C:139-150)
;
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_PHOLE
65-75
2
-
B:43-53
C:43-53
2
SOD_CU_ZN_2
PS00332
Copper/Zinc superoxide dismutase signature 2.
SODC_PHOLE
161-172
2
-
B:139-150
C:139-150
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1yaia_ (A:)
1b: SCOP_d1yaib_ (B:)
1c: SCOP_d1yaic_ (C:)
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)
Photobacterium leiognathi [TaxId: 553611]
(9)
1a
d1yaia_
A:
1b
d1yaib_
B:
1c
d1yaic_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1yaiA00 (A:1-151)
1b: CATH_1yaiB00 (B:1-151)
1c: CATH_1yaiC00 (C:2-151)
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)
Photobacterium leiognathi. Organism_taxid: 658. Strain: mc1061.
(1)
1a
1yaiA00
A:1-151
1b
1yaiB00
B:1-151
1c
1yaiC00
C:2-151
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Sod_Cu_1yaiC01 (C:2-150)
1b: PFAM_Sod_Cu_1yaiC02 (C:2-150)
1c: PFAM_Sod_Cu_1yaiC03 (C:2-150)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sod_Cu]
(71)
Family
:
Sod_Cu
(71)
Photobacterium leiognathi
(3)
1a
Sod_Cu-1yaiC01
C:2-150
1b
Sod_Cu-1yaiC02
C:2-150
1c
Sod_Cu-1yaiC03
C:2-150
[
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 B
Chain C
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 (80 KB)
Header - Asym.Unit
Biol.Unit 1 (51 KB)
Header - Biol.Unit 1
Biol.Unit 2 (51 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
1YAI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
