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.
1OBX
Asym. Unit
Info
Asym.Unit (36 KB)
Biol.Unit 1 (61 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 THE COMPLEX OF PDZ2 OF SYNTENIN WITH AN INTERLEUKIN 5 RECEPTOR ALPHA PEPTIDE.
Authors
:
B. S. Kang, D. R. Cooper, Y. Devedjiev, U. Derewenda, Z. S. Derewenda
Date
:
31 Jan 03 (Deposition) - 10 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.35
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Cell Adhesion, Adhesion/Complex, Pdz Domain, Signal Transduction, Nuclear Protein,
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. S. Kang, D. R. Cooper, Y. Devedjiev, U. Derewenda, Z. S. Derewenda
Molecular Roots Of Degenerate Specificity In Syntenin'S Pdz2 Domain: Reassessment Of The Pdz Recognition Paradigm
Structure V. 11 845 2003
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
2
Ligand/Ion
COBALT (II) ION
2
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:208 , HOH A:2121 , HOH A:2122 , HOH A:2123 , ASP B:5 , HOH B:2001 , HOH B:2002
BINDING SITE FOR RESIDUE CO A1271
2
AC2
SOFTWARE
HIS A:236 , HOH A:2124 , HOH A:2125
BINDING SITE FOR RESIDUE CO A1272
3
AC3
SOFTWARE
HIS A:202 , SER A:226 , ARG A:229 , ASN A:230 , LYS A:250 , GLN A:253 , HOH A:2126 , HOH A:2127
BINDING SITE FOR RESIDUE SO4 A1273
4
AC4
SOFTWARE
ASP A:251 , SER A:252 , HOH A:2098 , HOH A:2132 , HOH A:2133 , HOH A:2134 , HOH A:2135
BINDING SITE FOR RESIDUE SO4 A1274
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDZ (-|A:198-270)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDZ
PS50106
PDZ domain profile.
SDCB1_HUMAN
114-193
198-273
1
-
A:198-270
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.16a (B:5-8)
Exon 2.8a (A:197-250)
Exon 2.9 (A:251-270)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.14/1.16a
2: Boundary 1.16a/-
3: Boundary 2.7c/2.8a
4: Boundary 2.8a/2.9
5: Boundary 2.9/2.10h
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
1.2f
ENST00000256452
2f
ENSE00001898297
chr3:
3151664-3151629
36
IL5RA_HUMAN
-
0
0
-
-
1.3b
ENST00000256452
3b
ENSE00000997127
chr3:
3150375-3150234
142
IL5RA_HUMAN
-
0
0
-
-
1.4
ENST00000256452
4
ENSE00001322495
chr3:
3147220-3147152
69
IL5RA_HUMAN
-
0
0
-
-
1.5
ENST00000256452
5
ENSE00002175535
chr3:
3146671-3146587
85
IL5RA_HUMAN
1-28
28
0
-
-
1.6
ENST00000256452
6
ENSE00001624596
chr3:
3144504-3144359
146
IL5RA_HUMAN
28-76
49
0
-
-
1.7b
ENST00000256452
7b
ENSE00001730405
chr3:
3143514-3143376
139
IL5RA_HUMAN
77-123
47
0
-
-
1.8
ENST00000256452
8
ENSE00001634426
chr3:
3139974-3139821
154
IL5RA_HUMAN
123-174
52
0
-
-
1.9b
ENST00000256452
9b
ENSE00001733184
chr3:
3139741-3139554
188
IL5RA_HUMAN
174-237
64
0
-
-
1.10
ENST00000256452
10
ENSE00001619473
chr3:
3137128-3136983
146
IL5RA_HUMAN
237-285
49
0
-
-
1.11a
ENST00000256452
11a
ENSE00001657506
chr3:
3134046-3133908
139
IL5RA_HUMAN
286-332
47
0
-
-
1.13
ENST00000256452
13
ENSE00000912359
chr3:
3118311-3118215
97
IL5RA_HUMAN
332-364
33
0
-
-
1.14
ENST00000256452
14
ENSE00000912357
chr3:
3116550-3116466
85
IL5RA_HUMAN
364-392
29
0
-
-
1.16a
ENST00000256452
16a
ENSE00001908764
chr3:
3111995-3111421
575
IL5RA_HUMAN
393-420
28
1
B:5-8
4
2.1b
ENST00000260130
1b
ENSE00001423873
chr8:
59465728-59465862
135
SDCB1_HUMAN
-
0
0
-
-
2.3c
ENST00000260130
3c
ENSE00002198946
chr8:
59477578-59477643
66
SDCB1_HUMAN
1-17
17
0
-
-
2.4b
ENST00000260130
4b
ENSE00000928399
chr8:
59483446-59483524
79
SDCB1_HUMAN
18-44
27
0
-
-
2.5c
ENST00000260130
5c
ENSE00000928400
chr8:
59484764-59484873
110
SDCB1_HUMAN
44-80
37
0
-
-
2.6a
ENST00000260130
6a
ENSE00000928401
chr8:
59488459-59488620
162
SDCB1_HUMAN
81-134
54
0
-
-
2.7c
ENST00000260130
7c
ENSE00000928402
chr8:
59490592-59490767
176
SDCB1_HUMAN
135-193
59
0
-
-
2.8a
ENST00000260130
8a
ENSE00000928403
chr8:
59492182-59492353
172
SDCB1_HUMAN
193-250
58
1
A:197-250
54
2.9
ENST00000260130
9
ENSE00000928404
chr8:
59493076-59493167
92
SDCB1_HUMAN
251-281
31
1
A:251-270
20
2.10h
ENST00000260130
10h
ENSE00002117339
chr8:
59494245-59495419
1175
SDCB1_HUMAN
281-298
18
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1obxa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PDZ domain-like
(299)
Superfamily
:
PDZ domain-like
(299)
Family
:
PDZ domain
(180)
Protein domain
:
Syntenin 1
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d1obxa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1obxA00 (A:197-270)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Pdz3 Domain
(191)
Homologous Superfamily
:
[code=2.30.42.10, no name defined]
(191)
Human (Homo sapiens)
(120)
1a
1obxA00
A:197-270
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PDZ_1obxA01 (A:198-270)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PDZ-like
(184)
Family
:
PDZ
(172)
Homo sapiens (Human)
(96)
1a
PDZ-1obxA01
A:198-270
[
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
Chain B
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 (36 KB)
Header - Asym.Unit
Biol.Unit 1 (61 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
1OBX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
