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.
2YRD
Asym. Unit
Info
Asym.Unit (293 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 ZF-SEC23_SEC24 FROM HUMAN SEC23A MUTANT V69A
Authors
:
T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
02 Apr 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Zinc Binding, Copii, Coat Protein Complex-Ii, Endoplasmic Reticulum, Golgi, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Zf-Sec23_sec24 From Human Sec23A Mutant V69A
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.2b (A:50-74 (gaps))
Exon 1.3 (A:74-93)
Exon 1.4 (A:94-108)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1b/1.2b
2: Boundary 1.2b/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5a
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
1.1b
ENST00000307712
1b
ENSE00001375759
chr14:
39572439-39572236
204
SC23A_HUMAN
-
0
0
-
-
1.2b
ENST00000307712
2b
ENSE00000889778
chr14:
39565343-39565102
242
SC23A_HUMAN
1-74
74
1
A:50-74 (gaps)
50
1.3
ENST00000307712
3
ENSE00001790491
chr14:
39562448-39562391
58
SC23A_HUMAN
74-93
20
1
A:74-93
20
1.4
ENST00000307712
4
ENSE00000889776
chr14:
39561831-39561745
87
SC23A_HUMAN
94-122
29
1
A:94-108
15
1.5a
ENST00000307712
5a
ENSE00000889775
chr14:
39560917-39560681
237
SC23A_HUMAN
123-201
79
0
-
-
1.6
ENST00000307712
6
ENSE00000656388
chr14:
39556212-39556133
80
SC23A_HUMAN
202-228
27
0
-
-
1.7
ENST00000307712
7
ENSE00001665685
chr14:
39555110-39554966
145
SC23A_HUMAN
228-276
49
0
-
-
1.8
ENST00000307712
8
ENSE00000889773
chr14:
39545297-39545139
159
SC23A_HUMAN
277-329
53
0
-
-
1.9
ENST00000307712
9
ENSE00000656385
chr14:
39543734-39543619
116
SC23A_HUMAN
330-368
39
0
-
-
1.10
ENST00000307712
10
ENSE00000656384
chr14:
39536500-39536377
124
SC23A_HUMAN
368-409
42
0
-
-
1.11
ENST00000307712
11
ENSE00000656383
chr14:
39534197-39534117
81
SC23A_HUMAN
410-436
27
0
-
-
1.12
ENST00000307712
12
ENSE00000656382
chr14:
39532617-39532528
90
SC23A_HUMAN
437-466
30
0
-
-
1.13
ENST00000307712
13
ENSE00000656381
chr14:
39531075-39530969
107
SC23A_HUMAN
467-502
36
0
-
-
1.14a
ENST00000307712
14a
ENSE00000889767
chr14:
39524500-39524347
154
SC23A_HUMAN
502-553
52
0
-
-
1.15
ENST00000307712
15
ENSE00000656378
chr14:
39517933-39517856
78
SC23A_HUMAN
554-579
26
0
-
-
1.16
ENST00000307712
16
ENSE00000889765
chr14:
39514528-39514367
162
SC23A_HUMAN
580-633
54
0
-
-
1.17
ENST00000307712
17
ENSE00000889764
chr14:
39512076-39511990
87
SC23A_HUMAN
634-662
29
0
-
-
1.18
ENST00000307712
18
ENSE00000656375
chr14:
39510091-39509936
156
SC23A_HUMAN
663-714
52
0
-
-
1.19
ENST00000307712
19
ENSE00000656374
chr14:
39508300-39508235
66
SC23A_HUMAN
715-736
22
0
-
-
1.20
ENST00000307712
20
ENSE00001134880
chr14:
39502532-39501124
1409
SC23A_HUMAN
737-765
29
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_zf_Sec23_Sec24_2yrdA01 (A:57-98)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: zf-Sec23_Sec24]
(8)
Family
:
zf-Sec23_Sec24
(8)
Homo sapiens (Human)
(4)
1a
zf-Sec23_Sec24-2yrdA01
A:57-98
[
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 (293 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
2YRD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
