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.
2DDA
Biol. Unit 4
Info
Asym.Unit (148 KB)
Biol.Unit 1 (39 KB)
Biol.Unit 2 (38 KB)
Biol.Unit 3 (39 KB)
Biol.Unit 4 (38 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 PSEUDECHETOXIN FROM PSEUDECHIS AUSTRALIS
Authors
:
N. Suzuki, Y. Yamazaki, Z. Fujimoto, T. Morita, H. Mizuno
Date
:
25 Jan 06 (Deposition) - 30 Jan 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Crisp, Snake Venom, Cng Channel, Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Suzuki, Y. Yamazaki, R. L. Brown, Z. Fujimoto, T. Morita, H. Mizuno
Structures Of Pseudechetoxin And Pseudecin, Two Snake-Venom Cysteine-Rich Secretory Proteins That Target Cyclic Nucleotide-Gated Ion Channels: Implications For Movement Of The C-Terminal Cysteine-Rich Domain
Acta Crystallogr. , Sect. D V. 64 1034 2008
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
1b: FORMIC ACID (FMTb)
1c: FORMIC ACID (FMTc)
1d: FORMIC ACID (FMTd)
1e: FORMIC ACID (FMTe)
1f: FORMIC ACID (FMTf)
2a: GLYCEROL (GOLa)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
1
Ligand/Ion
FORMIC ACID
2
GOL
-1
Ligand/Ion
GLYCEROL
3
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC8 (SOFTWARE)
3: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
HOH C:496 , SER D:73 , GLN D:74 , SER D:128 , HOH D:532 , HOH D:597
BINDING SITE FOR RESIDUE NA D 304
2
AC8
SOFTWARE
SER A:184 , LYS A:187 , SER D:103 , VAL D:104 , ILE D:105 , GLY D:106
BINDING SITE FOR RESIDUE FMT D 308
3
BC1
SOFTWARE
ALA A:51 , HIS A:52 , SER D:189 , THR D:193
BINDING SITE FOR RESIDUE FMT A 310
[
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: CRISP_1 (D:106-116)
2: CRISP_2 (D:132-143)
3: SHKT (D:173-206)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CRISP_1
PS01009
CRISP family signature 1.
CRVP_PSEAU
133-143
1
-
-
-
D:106-116
2
CRISP_2
PS01010
CRISP family signature 2.
CRVP_PSEAU
159-170
1
-
-
-
D:132-143
3
SHKT
PS51670
ShKT domain profile.
CRVP_PSEAU
200-233
1
-
-
-
D:173-206
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2ddaa1 (A:4-154)
1b: SCOP_d2ddab1 (B:4-154)
1c: SCOP_d2ddac1 (C:4-154)
1d: SCOP_d2ddad1 (D:4-154)
2a: SCOP_d2ddaa2 (A:155-211)
2b: SCOP_d2ddab2 (B:155-211)
2c: SCOP_d2ddac2 (C:155-211)
2d: SCOP_d2ddad2 (D:155-211)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
PR-1-like
(14)
Superfamily
:
PR-1-like
(14)
Family
:
automated matches
(4)
Protein domain
:
automated matches
(4)
Pseudechis australis [TaxId: 8670]
(1)
1a
d2ddaa1
A:4-154
1b
d2ddab1
B:4-154
1c
d2ddac1
C:4-154
1d
d2ddad1
D:4-154
Class
:
Small proteins
(3458)
Fold
:
Crisp domain-like
(13)
Superfamily
:
Crisp domain-like
(13)
Family
:
automated matches
(8)
Protein domain
:
automated matches
(8)
Pseudechis australis [TaxId: 8670]
(1)
2a
d2ddaa2
A:155-211
2b
d2ddab2
B:155-211
2c
d2ddac2
C:155-211
2d
d2ddad2
D:155-211
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2ddaA01 (A:4-170)
1b: CATH_2ddaB01 (B:4-170)
1c: CATH_2ddaC01 (C:4-170)
1d: CATH_2ddaD01 (D:4-170)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Pathogenesis-related Protein p14a
(12)
Homologous Superfamily
:
Pathogenesis-related Protein p14a
(12)
Mulga snake (Pseudechis australis)
(1)
1a
2ddaA01
A:4-170
1b
2ddaB01
B:4-170
1c
2ddaC01
C:4-170
1d
2ddaD01
D:4-170
[
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 D
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 (148 KB)
Header - Asym.Unit
Biol.Unit 1 (39 KB)
Header - Biol.Unit 1
Biol.Unit 2 (38 KB)
Header - Biol.Unit 2
Biol.Unit 3 (39 KB)
Header - Biol.Unit 3
Biol.Unit 4 (38 KB)
Header - Biol.Unit 4
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
2DDA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
