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.
1RFJ
Asym. Unit
Info
Asym.Unit (32 KB)
Biol.Unit 1 (28 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 POTATO CALMODULIN PCM6
Authors
:
D. C. Liang, C. H. Yun, W. R. Chang
Date
:
10 Nov 03 (Deposition) - 29 Jun 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Plant Calmodulin, Crystal Structure, Pcm6, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. H. Yun, J. Bai, D. Y. Sun, D. F. Cui, W. R. Chang, D. C. Liang
Structure Of Potato Calmodulin Pcm6: The First Report Of The Three-Dimensional Structure Of A Plant Calmodulin.
Acta Crystallogr. , Sect. D V. 60 1214 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 7)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
MPD
3
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:20 , ASP A:22 , ASP A:24 , CYS A:26 , GLU A:31 , HOH A:4109
BINDING SITE FOR RESIDUE CA A 1001
2
AC2
SOFTWARE
ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67 , HOH A:4056
BINDING SITE FOR RESIDUE CA A 1002
3
AC3
SOFTWARE
ASP A:93 , ASP A:95 , ASN A:97 , PHE A:99 , GLU A:104 , HOH A:4063
BINDING SITE FOR RESIDUE CA A 1003
4
AC4
SOFTWARE
ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140 , HOH A:4062
BINDING SITE FOR RESIDUE CA A 1004
5
AC5
SOFTWARE
LYS A:86 , PHE A:89 , HOH A:4022
BINDING SITE FOR RESIDUE MPD A 2001
6
AC6
SOFTWARE
LEU A:105 , ALA A:128 , MET A:145
BINDING SITE FOR RESIDUE MPD A 3001
7
AC7
SOFTWARE
PRO A:66 , GLN A:96 , ASP A:122 , ARG A:126 , GLY A:134 , HOH A:4023 , HOH A:4047
BINDING SITE FOR RESIDUE MPD A 4001
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (A:7-42|A:43-78|A:80-115|A:116-147)
2: EF_HAND_1 (A:20-32|A:56-68|A:93-105|A:129-141)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
CALM5_SOLTU
8-43
44-79
81-116
117-149
4
A:7-42
A:43-78
A:80-115
A:116-147
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
CALM5_SOLTU
21-33
57-69
94-106
130-142
4
A:20-32
A:56-68
A:93-105
A:129-141
[
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, 1)
Info
All SCOP Domains
1a: SCOP_d1rfja_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Calmodulin-like
(356)
Protein domain
:
Calmodulin
(152)
Potato (Solanum tuberosum) [TaxId: 4113]
(1)
1a
d1rfja_
A:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1rfjA01 (A:0-77)
1b: CATH_1rfjA02 (A:78-147)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Potato (Solanum tuberosum)
(1)
1a
1rfjA01
A:0-77
1b
1rfjA02
A:78-147
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_EF_hand_5_1rfjA01 (A:84-145)
1b: PFAM_EF_hand_5_1rfjA02 (A:84-145)
2a: PFAM_EF_hand_6_1rfjA03 (A:96-147)
2b: PFAM_EF_hand_6_1rfjA04 (A:96-147)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EF_hand
(270)
Family
:
EF_hand_5
(126)
Solanum tuberosum (Potato)
(1)
1a
EF_hand_5-1rfjA01
A:84-145
1b
EF_hand_5-1rfjA02
A:84-145
Family
:
EF_hand_6
(75)
Solanum tuberosum (Potato)
(1)
2a
EF_hand_6-1rfjA03
A:96-147
2b
EF_hand_6-1rfjA04
A:96-147
[
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
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 (32 KB)
Header - Asym.Unit
Biol.Unit 1 (28 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
1RFJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help