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.
2Z4F
Asym. Unit
Info
Asym.Unit (849 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 DISCOIDIN DOMAIN OF DDR2
Authors
:
O. Ichikawa, M. Osawa, N. Nishida, N. Goshima, N. Nomura, I. Shimada
Date
:
16 Jun 07 (Deposition) - 04 Sep 07 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Beta Barrel, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Ichikawa, M. Osawa, N. Nishida, N. Goshima, N. Nomura, I. Shimada
Structural Basis Of The Collagen-Binding Mode Of Discoidin Domain Receptor 2
Embo J. V. 26 4168 2007
(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_041498 (R105S, chain A, )
2: VAR_065719 (E113K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_041498
R
105
S
DDR2_HUMAN
Unclassified
---
A
R
105
S
2
UniProt
VAR_065719
E
113
K
DDR2_HUMAN
Disease (SEMD-SL)
---
A
E
113
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: FA58C_3 (A:30-185)
2: FA58C_1 (A:71-104)
3: FA58C_2 (A:168-185)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FA58C_3
PS50022
Coagulation factors 5/8 type C domain (FA58C) profile.
DDR2_HUMAN
30-185
1
A:30-185
2
FA58C_1
PS01285
Coagulation factors 5/8 type C domain (FA58C) signature 1.
DDR2_HUMAN
71-104
1
A:71-104
3
FA58C_2
PS01286
Coagulation factors 5/8 type C domain (FA58C) signature 2.
DDR2_HUMAN
168-185
1
A:168-185
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.6 (A:26-28)
Exon 1.7 (A:28-62)
Exon 1.8b (A:62-139)
Exon 1.9b (A:140-186)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5/1.6
2: Boundary 1.6/1.7
3: Boundary 1.7/1.8b
4: Boundary 1.8b/1.9b
5: Boundary 1.9b/1.10
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
1.3a
ENST00000367922
3a
ENSE00001445934
chr1:
162602255-162602421
167
DDR2_HUMAN
-
0
0
-
-
1.4
ENST00000367922
4
ENSE00001165699
chr1:
162625001-162625164
164
DDR2_HUMAN
-
0
0
-
-
1.5
ENST00000367922
5
ENSE00001220765
chr1:
162674842-162674921
80
DDR2_HUMAN
-
0
0
-
-
1.6
ENST00000367922
6
ENSE00000983497
chr1:
162688827-162688935
109
DDR2_HUMAN
1-28
28
1
A:26-28
3
1.7
ENST00000367922
7
ENSE00001165692
chr1:
162722885-162722987
103
DDR2_HUMAN
28-62
35
1
A:28-62
35
1.8b
ENST00000367922
8b
ENSE00001165686
chr1:
162724414-162724645
232
DDR2_HUMAN
62-139
78
1
A:62-139
78
1.9b
ENST00000367922
9b
ENSE00001165680
chr1:
162724946-162725093
148
DDR2_HUMAN
140-189
50
1
A:140-186
47
1.10
ENST00000367922
10
ENSE00001165673
chr1:
162725454-162725559
106
DDR2_HUMAN
189-224
36
0
-
-
1.11
ENST00000367922
11
ENSE00001165667
chr1:
162729586-162729769
184
DDR2_HUMAN
224-285
62
0
-
-
1.12
ENST00000367922
12
ENSE00001068052
chr1:
162731001-162731244
244
DDR2_HUMAN
286-367
82
0
-
-
1.13
ENST00000367922
13
ENSE00001165652
chr1:
162735791-162735853
63
DDR2_HUMAN
367-388
22
0
-
-
1.14a
ENST00000367922
14a
ENSE00001165641
chr1:
162737019-162737149
131
DDR2_HUMAN
388-431
44
0
-
-
1.15a
ENST00000367922
15a
ENSE00001165634
chr1:
162740092-162740302
211
DDR2_HUMAN
432-502
71
0
-
-
1.16a
ENST00000367922
16a
ENSE00001165626
chr1:
162741814-162742037
224
DDR2_HUMAN
502-576
75
0
-
-
1.17
ENST00000367922
17
ENSE00001165621
chr1:
162743259-162743386
128
DDR2_HUMAN
577-619
43
0
-
-
1.18
ENST00000367922
18
ENSE00001165614
chr1:
162745442-162745633
192
DDR2_HUMAN
619-683
65
0
-
-
1.19
ENST00000367922
19
ENSE00001165607
chr1:
162745926-162746160
235
DDR2_HUMAN
683-761
79
0
-
-
1.20
ENST00000367922
20
ENSE00001165603
chr1:
162748370-162748519
150
DDR2_HUMAN
762-811
50
0
-
-
1.21b
ENST00000367922
21b
ENSE00001170600
chr1:
162749902-162750237
336
DDR2_HUMAN
812-855
44
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2z4fa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d2z4fa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2z4fA00 (A:26-186)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Human (Homo sapiens)
(39)
1a
2z4fA00
A:26-186
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_F5_F8_type_C_2z4fA01 (A:45-182)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Homo sapiens (Human)
(10)
1a
F5_F8_type_C-2z4fA01
A:45-182
[
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 (849 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
2Z4F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
