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.
4DGP
Asym. Unit
Info
Asym.Unit (90 KB)
Biol.Unit 1 (86 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE WILD-TYPE SRC HOMOLOGY 2 (SH2)-DOMAIN CONTAINING PROTEIN TYROSINE PHOSPHATASE-2 (SHP2)
Authors
:
Z. H. Yu, J. Xu, C. D. Walls, L. Chen, S. Zhang, L. Wu, L. N. Wang, S. J. Liu, Z
Date
:
26 Jan 12 (Deposition) - 06 Mar 13 (Release) - 01 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. H. Yu, J. Xu, C. D. Walls, L. Chen, S. Zhang, R. Zhang, L. Wu, L. Wang, S. Liu, Z. Y. Zhang
Structural And Mechanistic Insights Into Leopard Syndrome-Associated Shp2 Mutations.
J. Biol. Chem. V. 288 10472 2013
[
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
(53, 53)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_015601 (T42A, chain A, )
02: VAR_027184 (N58K, chain A, )
03: VAR_066060 (T59A, chain A, )
04: VAR_015602 (G60A, chain A, )
05: VAR_015990 (G60V, chain A, )
06: VAR_015603 (D61G, chain A, )
07: VAR_015604 (D61N, chain A, )
08: VAR_015991 (D61V, chain A, )
09: VAR_015992 (D61Y, chain A, )
10: VAR_015605 (Y62D, chain A, )
11: VAR_015606 (Y63C, chain A, )
12: VAR_015993 (E69K, chain A, )
13: VAR_027185 (E69Q, chain A, )
14: VAR_015994 (F71K, chain A, )
15: VAR_015995 (F71L, chain A, )
16: VAR_015607 (A72G, chain A, )
17: VAR_015608 (A72S, chain A, )
18: VAR_015996 (A72T, chain A, )
19: VAR_015997 (A72V, chain A, )
20: VAR_015609 (T73I, chain A, )
21: VAR_015998 (E76A, chain A, )
22: VAR_015610 (E76D, chain A, )
23: VAR_015999 (E76G, chain A, )
24: VAR_016000 (E76K, chain A, )
25: VAR_016001 (E76V, chain A, )
26: VAR_027186 (Q79P, chain A, )
27: VAR_015611 (Q79R, chain A, )
28: VAR_015612 (D106A, chain A, )
29: VAR_015613 (E139D, chain A, )
30: VAR_027187 (Q256R, chain A, )
31: VAR_015614 (Y279C, chain A, )
32: VAR_027188 (Y279S, chain A, )
33: VAR_015615 (I282V, chain A, )
34: VAR_015617 (F285L, chain A, )
35: VAR_015616 (F285S, chain A, )
36: VAR_015619 (N308D, chain A, )
37: VAR_015618 (N308S, chain A, )
38: VAR_015620 (I309V, chain A, )
39: VAR_027189 (T411M, chain A, )
40: VAR_027190 (A461T, chain A, )
41: VAR_027191 (G464A, chain A, )
42: VAR_015621 (T468M, chain A, )
43: VAR_071706 (P491S, chain A, )
44: VAR_027192 (R498L, chain A, )
45: VAR_027193 (R498W, chain A, )
46: VAR_015622 (R501K, chain A, )
47: VAR_015623 (S502T, chain A, )
48: VAR_016002 (G503A, chain A, )
49: VAR_016003 (G503R, chain A, )
50: VAR_015624 (M504V, chain A, )
51: VAR_027194 (Q506P, chain A, )
52: VAR_027195 (Q506R, chain A, )
53: VAR_027196 (Q510P, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_015601
T
42
A
PTN11_HUMAN
Disease (NS1)
---
A
T
42
A
02
UniProt
VAR_027184
N
58
K
PTN11_HUMAN
Disease (NS1)
---
A
N
58
K
03
UniProt
VAR_066060
T
59
A
PTN11_HUMAN
Disease (NS1)
---
A
T
59
A
04
UniProt
VAR_015602
G
60
A
PTN11_HUMAN
Disease (NS1)
---
A
G
60
A
05
UniProt
VAR_015990
G
60
V
PTN11_HUMAN
Unclassified
---
A
G
60
V
06
UniProt
VAR_015603
D
61
G
PTN11_HUMAN
Disease (NS1)
---
A
D
61
G
07
UniProt
VAR_015604
D
61
N
PTN11_HUMAN
Disease (NS1)
---
A
D
61
N
08
UniProt
VAR_015991
D
61
V
PTN11_HUMAN
Disease (JMML)
---
A
D
61
V
09
UniProt
VAR_015992
D
61
Y
PTN11_HUMAN
Disease (JMML)
---
A
D
61
Y
10
UniProt
VAR_015605
Y
62
D
PTN11_HUMAN
Disease (NS1)
---
A
Y
62
D
11
UniProt
VAR_015606
Y
63
C
PTN11_HUMAN
Disease (NS1)
---
A
Y
63
C
12
UniProt
VAR_015993
E
69
K
PTN11_HUMAN
Disease (JMML)
---
A
E
69
K
13
UniProt
VAR_027185
E
69
Q
PTN11_HUMAN
Disease (NS1)
---
A
E
69
Q
14
UniProt
VAR_015994
F
71
K
PTN11_HUMAN
Unclassified
---
A
F
71
K
15
UniProt
VAR_015995
F
71
L
PTN11_HUMAN
Unclassified
---
A
F
71
L
16
UniProt
VAR_015607
A
72
G
PTN11_HUMAN
Disease (NS1)
---
A
A
72
G
17
UniProt
VAR_015608
A
72
S
PTN11_HUMAN
Disease (NS1)
---
A
A
72
S
18
UniProt
VAR_015996
A
72
T
PTN11_HUMAN
Disease (JMML)
---
A
A
72
T
19
UniProt
VAR_015997
A
72
V
PTN11_HUMAN
Disease (JMML)
---
A
A
72
V
20
UniProt
VAR_015609
T
73
I
PTN11_HUMAN
Disease (NS1)
28933387
A
T
73
I
21
UniProt
VAR_015998
E
76
A
PTN11_HUMAN
Disease (JMML)
---
A
E
76
A
22
UniProt
VAR_015610
E
76
D
PTN11_HUMAN
Disease (NS1)
---
A
E
76
D
23
UniProt
VAR_015999
E
76
G
PTN11_HUMAN
Disease (JMML)
---
A
E
76
G
24
UniProt
VAR_016000
E
76
K
PTN11_HUMAN
Disease (JMML)
28933388
A
E
76
K
25
UniProt
VAR_016001
E
76
V
PTN11_HUMAN
Disease (JMML)
---
A
E
76
V
26
UniProt
VAR_027186
Q
79
P
PTN11_HUMAN
Disease (NS1)
---
A
Q
79
P
27
UniProt
VAR_015611
Q
79
R
PTN11_HUMAN
Disease (NS1)
---
A
Q
79
R
28
UniProt
VAR_015612
D
106
A
PTN11_HUMAN
Disease (NS1)
---
A
D
106
A
29
UniProt
VAR_015613
E
139
D
PTN11_HUMAN
Disease (NS1)
---
A
E
139
D
30
UniProt
VAR_027187
Q
256
R
PTN11_HUMAN
Disease (NS1)
---
A
Q
256
R
31
UniProt
VAR_015614
Y
279
C
PTN11_HUMAN
Disease (NS1)
---
A
Y
279
C
32
UniProt
VAR_027188
Y
279
S
PTN11_HUMAN
Disease (LPRD1)
---
A
Y
279
S
33
UniProt
VAR_015615
I
282
V
PTN11_HUMAN
Disease (NS1)
---
A
I
282
V
34
UniProt
VAR_015617
F
285
L
PTN11_HUMAN
Disease (NS1)
---
A
F
285
L
35
UniProt
VAR_015616
F
285
S
PTN11_HUMAN
Disease (NS1)
---
A
F
285
S
36
UniProt
VAR_015619
N
308
D
PTN11_HUMAN
Disease (NS1)
---
A
N
308
D
37
UniProt
VAR_015618
N
308
S
PTN11_HUMAN
Disease (NS1)
---
A
N
308
S
38
UniProt
VAR_015620
I
309
V
PTN11_HUMAN
Unclassified
201787206
A
I
309
V
39
UniProt
VAR_027189
T
415
M
PTN11_HUMAN
Disease (NS1)
---
A
T
411
M
40
UniProt
VAR_027190
A
465
T
PTN11_HUMAN
Disease (LPRD1)
---
A
A
461
T
41
UniProt
VAR_027191
G
468
A
PTN11_HUMAN
Disease (LPRD1)
---
A
G
464
A
42
UniProt
VAR_015621
T
472
M
PTN11_HUMAN
Disease (LPRD1)
---
A
T
468
M
43
UniProt
VAR_071706
P
495
S
PTN11_HUMAN
Disease (NS1)
---
A
P
491
S
44
UniProt
VAR_027192
R
502
L
PTN11_HUMAN
Disease (LPRD1)
---
A
R
498
L
45
UniProt
VAR_027193
R
502
W
PTN11_HUMAN
Disease (LPRD1)
---
A
R
498
W
46
UniProt
VAR_015622
R
505
K
PTN11_HUMAN
Disease (NS1)
---
A
R
501
K
47
UniProt
VAR_015623
S
506
T
PTN11_HUMAN
Disease (NS1)
---
A
S
502
T
48
UniProt
VAR_016002
G
507
A
PTN11_HUMAN
Disease (JMML)
---
A
G
503
A
49
UniProt
VAR_016003
G
507
R
PTN11_HUMAN
Disease (NS1)
---
A
G
503
R
50
UniProt
VAR_015624
M
508
V
PTN11_HUMAN
Disease (NS1)
---
A
M
504
V
51
UniProt
VAR_027194
Q
510
P
PTN11_HUMAN
Disease (LPRD1)
---
A
Q
506
P
52
UniProt
VAR_027195
Q
510
R
PTN11_HUMAN
Disease (NS1)
---
A
Q
506
R
53
UniProt
VAR_027196
Q
514
P
PTN11_HUMAN
Disease (LPRD1)
---
A
Q
510
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 5)
Info
All PROSITE Patterns/Profiles
1: SH2 (A:6-102|A:112-216)
2: TYR_PHOSPHATASE_PTP (A:247-521)
3: TYR_PHOSPHATASE_2 (A:436-512)
4: TYR_PHOSPHATASE_1 (A:457-467)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SH2
PS50001
Src homology 2 (SH2) domain profile.
PTN11_HUMAN
6-102
112-216
2
A:6-102
A:112-216
2
TYR_PHOSPHATASE_PTP
PS50055
PTP type protein phosphatase family profile.
PTN11_HUMAN
247-525
1
A:247-521
3
TYR_PHOSPHATASE_2
PS50056
Tyrosine specific protein phosphatases family profile.
PTN11_HUMAN
440-516
1
A:436-512
4
TYR_PHOSPHATASE_1
PS00383
Tyrosine specific protein phosphatases active site.
PTN11_HUMAN
461-471
1
A:457-467
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d4dgpa1 (A:3-110)
1b: SCOP_d4dgpa2 (A:111-218)
2a: SCOP_d4dgpa3 (A:219-528)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
SH2-like
(260)
Superfamily
:
SH2 domain
(260)
Family
:
automated matches
(35)
Protein domain
:
automated matches
(35)
Human (Homo sapiens) [TaxId: 9606]
(30)
1a
d4dgpa1
A:3-110
1b
d4dgpa2
A:111-218
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
(Phosphotyrosine protein) phosphatases II
(296)
Superfamily
:
(Phosphotyrosine protein) phosphatases II
(296)
Family
:
Higher-molecular-weight phosphotyrosine protein phosphatases
(166)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(21)
2a
d4dgpa3
A:219-528
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 (90 KB)
Header - Asym.Unit
Biol.Unit 1 (86 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
4DGP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
