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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2D9Z
Asym. Unit
Info
Asym.Unit (663 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(20 )
Title
:
SOLUTION STRUCTURE OF THE PH DOMAIN OF PROTEIN KINASE C, NU TYPE FROM HUMAN
Authors
:
H. Li, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
13 Dec 05 (Deposition) - 02 Jan 07 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Ph Domain, Protein Kinase C Nu Type, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Li, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Ph Domain Of Protein Kinase C, Nu Type From Human
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
1: VAR_061532 (L36I, chain A, )
2: VAR_037149 (S128R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_061532
L
445
I
KPCD3_HUMAN
Polymorphism
55912911
A
L
36
I
2
UniProt
VAR_037149
Q
546
R
KPCD3_HUMAN
Polymorphism
17856887
A
S
128
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PH_DOMAIN (A:8-123)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PH_DOMAIN
PS50003
PH domain profile.
KPCD3_HUMAN
416-532
1
A:8-123
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.11b (A:1-23 (gaps))
Exon 1.12 (A:24-49)
Exon 1.13a (A:50-129 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.10/1.11b
2: Boundary 1.11b/1.12
3: Boundary 1.12/1.13a
4: Boundary 1.13a/1.14a
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
1.3
ENST00000379066
3
ENSE00001479696
chr2:
37545037-37544930
108
KPCD3_HUMAN
-
0
0
-
-
1.4b
ENST00000379066
4b
ENSE00001479694
chr2:
37544322-37543380
943
KPCD3_HUMAN
1-96
96
0
-
-
1.5a
ENST00000379066
5a
ENSE00001706811
chr2:
37520414-37520276
139
KPCD3_HUMAN
97-143
47
0
-
-
1.6a
ENST00000379066
6a
ENSE00001758269
chr2:
37518142-37518011
132
KPCD3_HUMAN
143-187
45
0
-
-
1.7
ENST00000379066
7
ENSE00000747393
chr2:
37516656-37516499
158
KPCD3_HUMAN
187-239
53
0
-
-
1.8b
ENST00000379066
8b
ENSE00000747391
chr2:
37513512-37513320
193
KPCD3_HUMAN
240-304
65
0
-
-
1.9a
ENST00000379066
9a
ENSE00000747390
chr2:
37509762-37509685
78
KPCD3_HUMAN
304-330
27
0
-
-
1.10
ENST00000379066
10
ENSE00000747389
chr2:
37507072-37506889
184
KPCD3_HUMAN
330-391
62
0
-
-
1.11b
ENST00000379066
11b
ENSE00001802809
chr2:
37505132-37505009
124
KPCD3_HUMAN
391-432
42
1
A:1-23 (gaps)
40
1.12
ENST00000379066
12
ENSE00000747387
chr2:
37502987-37502910
78
KPCD3_HUMAN
433-458
26
1
A:24-49
26
1.13a
ENST00000379066
13a
ENSE00000747386
chr2:
37501840-37501564
277
KPCD3_HUMAN
459-551
93
1
A:50-129 (gaps)
89
1.14a
ENST00000379066
14a
ENSE00000747385
chr2:
37499575-37499523
53
KPCD3_HUMAN
551-568
18
0
-
-
1.15a
ENST00000379066
15a
ENSE00000747383
chr2:
37496830-37496758
73
KPCD3_HUMAN
569-593
25
0
-
-
1.16
ENST00000379066
16
ENSE00000747381
chr2:
37494679-37494573
107
KPCD3_HUMAN
593-628
36
0
-
-
1.17b
ENST00000379066
17b
ENSE00000747379
chr2:
37487527-37487366
162
KPCD3_HUMAN
629-682
54
0
-
-
1.18
ENST00000379066
18
ENSE00001604113
chr2:
37486824-37486726
99
KPCD3_HUMAN
683-715
33
0
-
-
1.19b
ENST00000379066
19b
ENSE00000747375
chr2:
37484072-37483805
268
KPCD3_HUMAN
716-805
90
0
-
-
1.20
ENST00000379066
20
ENSE00000747374
chr2:
37481432-37481347
86
KPCD3_HUMAN
805-833
29
0
-
-
1.21b
ENST00000379066
21b
ENSE00001479657
chr2:
37480493-37477645
2849
KPCD3_HUMAN
834-890
57
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2d9za_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PH domain-like barrel
(258)
Superfamily
:
PH domain-like
(257)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Human (Homo sapiens) [TaxId: 9606]
(30)
1a
d2d9za_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2d9zA01 (A:8-129)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
PH-domain like
(150)
Homologous Superfamily
:
Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
(147)
Human (Homo sapiens)
(85)
1a
2d9zA01
A:8-129
[
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
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 (663 KB)
Header - Asym.Unit
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
2D9Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
