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.
1UGK
Asym. Unit
Info
Asym.Unit (732 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 FIRST C2 DOMAIN OF SYNAPTOTAGMIN IV FROM HUMAN FETAL BRAIN (KIAA1342)
Authors
:
T. Nagashima, F. Hayashi, M. Shirouzu, T. Terada, T. Kigawa, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, H. Hirota, M. Yoshida, A. Tanaka, T. Osanai, Y. Matsuo, O. Ohara, T. Nagase, R. Kikuno, M. Nakayama, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
16 Jun 03 (Deposition) - 16 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Beta Sandwich, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Nagashima, F. Hayashi, M. Shirouzu, T. Terada, T. Kigawa, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, H. Hirota, M. Yoshida, A. Tanaka, T. Osanai, Y. Matsuo, O. Ohara, T. Nagase, R. Kikuno, M. Nakayama, S. Yokoyama
Solution Structure Of The First C2 Domain Of Synaptotagmin Iv From Human Fetal Brain (Kiaa1342)
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
(1, 1)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
1: VAR_052239 (S6N, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_052239
S
142
N
SYT4_HUMAN
Polymorphism
16977447
A
S
6
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: C2 (A:24-112|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
C2
PS50004
C2 domain profile.
SYT4_HUMAN
170-258
302-392
1
A:24-112
-
[
close PROSITE info
]
Exons
(2, 2)
Info
All Exons
Exon 1.2c (A:1-134 (gaps))
Exon 1.3a (A:135-138)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2c
2: Boundary 1.2c/1.3a
3: Boundary 1.3a/1.4
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
ENST00000255224
1
ENSE00001004031
chr18:
40857615-40857213
403
SYT4_HUMAN
1-12
12
0
-
-
1.2c
ENST00000255224
2c
ENSE00000668643
chr18:
40854359-40853545
815
SYT4_HUMAN
12-283
272
1
A:1-134 (gaps)
168
1.3a
ENST00000255224
3a
ENSE00000668642
chr18:
40851797-40851677
121
SYT4_HUMAN
284-324
41
1
A:135-138
4
1.4
ENST00000255224
4
ENSE00001140606
chr18:
40850613-40847859
2755
SYT4_HUMAN
324-425
102
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1ugka_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
C2 domain-like
(198)
Superfamily
:
C2 domain (Calcium/lipid-binding domain, CaLB)
(148)
Family
:
Synaptotagmin-like (S variant)
(38)
Protein domain
:
Synaptotagmin IV
(3)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1ugka_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1ugkA00 (A:1-138)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
C2- domain Calcium/lipid binding domain
(78)
Human (Homo sapiens)
(41)
1a
1ugkA00
A:1-138
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_C2_1ugkA01 (A:24-112)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
C2
(71)
Family
:
C2
(34)
Homo sapiens (Human)
(15)
1a
C2-1ugkA01
A:24-112
[
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 (732 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
1UGK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help