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.
1X5Z
Asym. Unit
Info
Asym.Unit (575 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 FIBRONECTIN TYPE-III DOMAIN OF HUMAN PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, D ISOFORM 4 VARIANT
Authors
:
M. Yoneyama, K. Saito, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
17 May 05 (Deposition) - 17 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Fibronectin Type Iii Domain Containing Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Yoneyama, K. Saito, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Fibronectin Type-Iii Domain Of Human Protein Tyrosine Phosphatase, Receptor Type, D Isoform 4 Variant
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
(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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: FN3 (-|-|A:20-109|A:112-114|-|-|-|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FN3
PS50853
Fibronectin type-III domain profile.
PTPRD_HUMAN
325-415
420-516
518-607
612-709
714-822
921-1016
823-916
1020-1106
2
-
-
A:20-109
A:112-114
-
-
-
-
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.20 (A:1-17)
Exon 1.21 (A:17-61)
Exon 1.22a (A:62-109)
Exon 1.23 (A:110-115)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.19b/1.20
2: Boundary 1.20/1.21
3: Boundary 1.21/1.22a
4: Boundary 1.22a/1.23
5: Boundary 1.23/1.24
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
ENST00000381196
1
ENSE00001811856
chr9:
9938610-9938507
104
PTPRD_HUMAN
-
0
0
-
-
1.2
ENST00000381196
2
ENSE00001948254
chr9:
9766851-9766810
42
PTPRD_HUMAN
-
0
0
-
-
1.3
ENST00000381196
3
ENSE00001955782
chr9:
9734571-9734533
39
PTPRD_HUMAN
-
0
0
-
-
1.4
ENST00000381196
4
ENSE00001889688
chr9:
9574781-9574732
50
PTPRD_HUMAN
-
0
0
-
-
1.6
ENST00000381196
6
ENSE00001817715
chr9:
9397482-9397449
34
PTPRD_HUMAN
-
0
0
-
-
1.7
ENST00000381196
7
ENSE00001940698
chr9:
9183363-9183304
60
PTPRD_HUMAN
-
0
0
-
-
1.8
ENST00000381196
8
ENSE00001487965
chr9:
9018735-9018697
39
PTPRD_HUMAN
-
0
0
-
-
1.10b
ENST00000381196
10b
ENSE00001254389
chr9:
8733946-8733780
167
PTPRD_HUMAN
1-22
22
0
-
-
1.11
ENST00000381196
11
ENSE00001172744
chr9:
8636844-8636699
146
PTPRD_HUMAN
22-70
49
0
-
-
1.12c
ENST00000381196
12c
ENSE00001172741
chr9:
8633458-8633317
142
PTPRD_HUMAN
71-118
48
0
-
-
1.13
ENST00000381196
13
ENSE00001172738
chr9:
8528779-8528591
189
PTPRD_HUMAN
118-181
64
0
-
-
1.15
ENST00000381196
15
ENSE00001780939
chr9:
8527353-8527345
9
PTPRD_HUMAN
181-184
4
0
-
-
1.16
ENST00000381196
16
ENSE00001739974
chr9:
8526644-8526627
18
PTPRD_HUMAN
184-190
7
0
-
-
1.17b
ENST00000381196
17b
ENSE00001087346
chr9:
8525035-8524925
111
PTPRD_HUMAN
190-227
38
0
-
-
1.18
ENST00000381196
18
ENSE00001662513
chr9:
8523524-8523513
12
PTPRD_HUMAN
227-231
5
0
-
-
1.19b
ENST00000381196
19b
ENSE00001087338
chr9:
8521546-8521277
270
PTPRD_HUMAN
231-321
91
0
-
-
1.20
ENST00000381196
20
ENSE00001012020
chr9:
8518429-8517848
582
PTPRD_HUMAN
321-515
195
1
A:1-17
17
1.21
ENST00000381196
21
ENSE00001172713
chr9:
8507434-8507301
134
PTPRD_HUMAN
515-559
45
1
A:17-61
45
1.22a
ENST00000381196
22a
ENSE00001368106
chr9:
8504405-8504261
145
PTPRD_HUMAN
560-608
49
1
A:62-109
48
1.23
ENST00000381196
23
ENSE00001012029
chr9:
8501059-8500754
306
PTPRD_HUMAN
608-710
103
1
A:110-115
6
1.24
ENST00000381196
24
ENSE00001012019
chr9:
8499840-8499647
194
PTPRD_HUMAN
710-774
65
0
-
-
1.25
ENST00000381196
25
ENSE00001172700
chr9:
8497268-8497242
27
PTPRD_HUMAN
775-783
9
0
-
-
1.26
ENST00000381196
26
ENSE00001012012
chr9:
8492979-8492862
118
PTPRD_HUMAN
784-823
40
0
-
-
1.27b
ENST00000381196
27b
ENSE00001012016
chr9:
8486349-8485762
588
PTPRD_HUMAN
823-1019
197
0
-
-
1.28b
ENST00000381196
28b
ENSE00001012033
chr9:
8485324-8485227
98
PTPRD_HUMAN
1019-1051
33
0
-
-
1.29b
ENST00000381196
29b
ENSE00001012014
chr9:
8484378-8484119
260
PTPRD_HUMAN
1052-1138
87
0
-
-
1.30
ENST00000381196
30
ENSE00001172680
chr9:
8471085-8470995
91
PTPRD_HUMAN
1138-1168
31
0
-
-
1.31
ENST00000381196
31
ENSE00001012036
chr9:
8465675-8465466
210
PTPRD_HUMAN
1169-1238
70
0
-
-
1.32
ENST00000381196
32
ENSE00001012037
chr9:
8460571-8460411
161
PTPRD_HUMAN
1239-1292
54
0
-
-
1.34
ENST00000381196
34
ENSE00001172661
chr9:
8449837-8449725
113
PTPRD_HUMAN
1292-1330
39
0
-
-
1.36
ENST00000381196
36
ENSE00001172655
chr9:
8436689-8436592
98
PTPRD_HUMAN
1330-1362
33
0
-
-
1.37
ENST00000381196
37
ENSE00001012032
chr9:
8404660-8404537
124
PTPRD_HUMAN
1363-1404
42
0
-
-
1.38
ENST00000381196
38
ENSE00001172638
chr9:
8389407-8389232
176
PTPRD_HUMAN
1404-1462
59
0
-
-
1.39
ENST00000381196
39
ENSE00001012031
chr9:
8376726-8376607
120
PTPRD_HUMAN
1463-1502
40
0
-
-
1.40
ENST00000381196
40
ENSE00001012034
chr9:
8376090-8375936
155
PTPRD_HUMAN
1503-1554
52
0
-
-
1.41
ENST00000381196
41
ENSE00001172619
chr9:
8341978-8341693
286
PTPRD_HUMAN
1554-1649
96
0
-
-
1.42
ENST00000381196
42
ENSE00001172611
chr9:
8341268-8341090
179
PTPRD_HUMAN
1650-1709
60
0
-
-
1.43
ENST00000381196
43
ENSE00001012021
chr9:
8340469-8340343
127
PTPRD_HUMAN
1709-1751
43
0
-
-
1.44
ENST00000381196
44
ENSE00001656481
chr9:
8339047-8338922
126
PTPRD_HUMAN
1752-1793
42
0
-
-
1.45
ENST00000381196
45
ENSE00001707976
chr9:
8331736-8331582
155
PTPRD_HUMAN
1794-1845
52
0
-
-
1.46
ENST00000381196
46
ENSE00001012025
chr9:
8319966-8319831
136
PTPRD_HUMAN
1845-1890
46
0
-
-
1.47c
ENST00000381196
47c
ENSE00001254378
chr9:
8317942-8314246
3697
PTPRD_HUMAN
1891-1912
22
0
-
-
1.49a
ENST00000381196
49a
ENSE00001922875
chr9:
10612509-10612398
112
PTPRD_HUMAN
-
0
0
-
-
1.50a
ENST00000381196
50a
ENSE00001820932
chr9:
10341062-10340963
100
PTPRD_HUMAN
-
0
0
-
-
1.51
ENST00000381196
51
ENSE00001895238
chr9:
10033790-10033718
73
PTPRD_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1x5za1 (A:8-109)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Fibronectin type III
(212)
Family
:
Fibronectin type III
(180)
Protein domain
:
Receptor-type tyrosine-protein phosphatase delta, PTPRD
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1x5za1
A:8-109
[
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_fn3_1x5zA01 (A:19-99)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
E-set
(290)
Family
:
fn3
(66)
Homo sapiens (Human)
(52)
1a
fn3-1x5zA01
A:19-99
[
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 (575 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
1X5Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help