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.
2QMS
Asym. Unit
Info
Asym.Unit (86 KB)
Biol.Unit 1 (41 KB)
Biol.Unit 2 (41 KB)
Biol.Unit 3 (42 KB)
Biol.Unit 4 (41 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 A SIGNALING MOLECULE
Authors
:
C. J. Porter, M. C. Wilce, J. A. Wilce
Date
:
16 Jul 07 (Deposition) - 22 Jul 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: A,B (1x)
Biol. Unit 4: C,D (1x)
Keywords
:
Sh2 Domain, Alpha/Beta Fold, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. J. Porter, J. M. Matthews, J. P. Mackay, S. E. Pursglove, J. W. Schmidberger, P. J. Leedman, S. C. Pero, D. N. Krag, M. C. Wilce, J. A. Wilce
Grb7 Sh2 Domain Structure And Interactions With A Cyclic Peptide Inhibitor Of Cancer Cell Migration And Proliferation.
Bmc Struct. Biol. V. 7 58 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 7)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG D:438 , ARG D:458 , SER D:460 , GLN D:461 , ARG D:462
BINDING SITE FOR RESIDUE SO4 D 301
2
AC2
SOFTWARE
ARG B:516 , CYS B:521 , LEU B:522 , ARG B:524
BINDING SITE FOR RESIDUE SO4 B 302
3
AC3
SOFTWARE
ARG A:462 , ARG A:516 , CYS A:521 , LEU A:522 , ARG A:524
BINDING SITE FOR RESIDUE SO4 A 303
4
AC4
SOFTWARE
HOH A:17 , HOH A:142 , ARG A:438 , ARG A:458 , SER A:460 , GLN A:461 , ARG A:462
BINDING SITE FOR RESIDUE SO4 A 305
5
AC5
SOFTWARE
HOH C:145 , ARG C:516 , CYS C:521 , LEU C:522 , ARG C:524
BINDING SITE FOR RESIDUE SO4 C 306
6
AC6
SOFTWARE
ARG B:438 , ARG B:458 , SER B:460 , GLN B:461
BINDING SITE FOR RESIDUE SO4 B 307
7
AC7
SOFTWARE
ARG C:438 , ARG C:458 , SER C:460 , GLN C:461 , ARG C:462
BINDING SITE FOR RESIDUE SO4 C 308
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: SH2 (A:431-527,B:431-527,C:431-527,D:43...)
;
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.
GRB7_HUMAN
431-527
4
A:431-527
B:431-527
C:431-527
D:431-527
[
close PROSITE info
]
Exons
(4, 16)
Info
All Exons
Exon 1.12 (A:420-424 | B:420-424 | C:420-424 ...)
Exon 1.13 (A:424-453 | B:424-453 | C:424-453 ...)
Exon 1.14 (A:453-484 | B:453-484 | C:453-484 ...)
Exon 1.15c (A:485-532 | B:485-532 | C:485-532 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.11/1.12
2: Boundary 1.12/1.13
3: Boundary 1.13/1.14
4: Boundary 1.14/1.15c
5: Boundary 1.15c/-
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
1.2
ENST00000394211
2
ENSE00001517752
chr17:
37894576-37894645
70
GRB7_HUMAN
-
0
0
-
-
1.4a
ENST00000394211
4a
ENSE00002183795
chr17:
37898505-37898709
205
GRB7_HUMAN
1-52
52
0
-
-
1.5a
ENST00000394211
5a
ENSE00001227713
chr17:
37898819-37898969
151
GRB7_HUMAN
52-102
51
0
-
-
1.5d
ENST00000394211
5d
ENSE00000950638
chr17:
37899151-37899307
157
GRB7_HUMAN
103-155
53
0
-
-
1.6a
ENST00000394211
6a
ENSE00000950639
chr17:
37899433-37899554
122
GRB7_HUMAN
155-195
41
0
-
-
1.6d
ENST00000394211
6d
ENSE00000950640
chr17:
37899646-37899723
78
GRB7_HUMAN
196-221
26
0
-
-
1.7a
ENST00000394211
7a
ENSE00000950641
chr17:
37900323-37900460
138
GRB7_HUMAN
222-267
46
0
-
-
1.8
ENST00000394211
8
ENSE00000950642
chr17:
37900806-37900916
111
GRB7_HUMAN
268-304
37
0
-
-
1.9
ENST00000394211
9
ENSE00000950643
chr17:
37901139-37901237
99
GRB7_HUMAN
305-337
33
0
-
-
1.10
ENST00000394211
10
ENSE00000950644
chr17:
37901496-37901576
81
GRB7_HUMAN
338-364
27
0
-
-
1.11
ENST00000394211
11
ENSE00000950645
chr17:
37901675-37901791
117
GRB7_HUMAN
365-403
39
0
-
-
1.12
ENST00000394211
12
ENSE00000950646
chr17:
37901981-37902041
61
GRB7_HUMAN
404-424
21
4
A:420-424
B:420-424
C:420-424
D:420-424
5
5
5
5
1.13
ENST00000394211
13
ENSE00000950647
chr17:
37902166-37902253
88
GRB7_HUMAN
424-453
30
4
A:424-453
B:424-453
C:424-453
D:424-453
30
30
30
30
1.14
ENST00000394211
14
ENSE00001651412
chr17:
37902362-37902455
94
GRB7_HUMAN
453-484
32
4
A:453-484
B:453-484
C:453-484
D:453-484
32
32
32
32
1.15c
ENST00000394211
15c
ENSE00001850980
chr17:
37903004-37903538
535
GRB7_HUMAN
485-532
48
4
A:485-532
B:485-532
C:485-532
D:485-532
48
48
48
48
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2qmsa_ (A:)
1b: SCOP_d2qmsb_ (B:)
1c: SCOP_d2qmsc_ (C:)
1d: SCOP_d2qmsd_ (D:)
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
:
SH2 domain
(225)
Protein domain
:
Growth factor receptor-bound protein 7
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d2qmsa_
A:
1b
d2qmsb_
B:
1c
d2qmsc_
C:
1d
d2qmsd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2qmsA00 (A:420-532)
1b: CATH_2qmsB00 (B:420-532)
1c: CATH_2qmsC00 (C:420-532)
1d: CATH_2qmsD00 (D:420-532)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
SHC Adaptor Protein
(206)
Homologous Superfamily
:
SHC Adaptor Protein
(206)
Human (Homo sapiens)
(147)
1a
2qmsA00
A:420-532
1b
2qmsB00
B:420-532
1c
2qmsC00
C:420-532
1d
2qmsD00
D:420-532
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_SH2_2qmsD01 (D:431-512)
1b: PFAM_SH2_2qmsD02 (D:431-512)
1c: PFAM_SH2_2qmsD03 (D:431-512)
1d: PFAM_SH2_2qmsD04 (D:431-512)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: SH2]
(119)
Family
:
SH2
(119)
Homo sapiens (Human)
(79)
1a
SH2-2qmsD01
D:431-512
1b
SH2-2qmsD02
D:431-512
1c
SH2-2qmsD03
D:431-512
1d
SH2-2qmsD04
D:431-512
[
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
Chain C
Chain D
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 (86 KB)
Header - Asym.Unit
Biol.Unit 1 (41 KB)
Header - Biol.Unit 1
Biol.Unit 2 (41 KB)
Header - Biol.Unit 2
Biol.Unit 3 (42 KB)
Header - Biol.Unit 3
Biol.Unit 4 (41 KB)
Header - Biol.Unit 4
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
2QMS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help