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.
1CD9
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (125 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR
Authors
:
M. Aritomi, N. Kunishima, T. Okamoto, R. Kuroki, Y. Ota, K. Morikawa
Date
:
08 Mar 99 (Deposition) - 08 Mar 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Class1 Cytokine, Hematopoietic Receptor, Signal Transduction, Cytokine
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Aritomi, N. Kunishima, T. Okamoto, R. Kuroki, Y. Ota, K. Morikawa
Atomic Structure Of The Gcsf-Receptor Complex Showing A New Cytokine-Receptor Recognition Scheme.
Nature V. 401 713 1999
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN B:10 , GLN B:25
BINDING SITE FOR RESIDUE NAG B 323
2
AC2
SOFTWARE
ASN D:10 , GLN D:25
BINDING SITE FOR RESIDUE NAG D 923
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_013073 (L125M, chain A/C, )
2: VAR_013074 (A142T, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_013073
L
157
M
CSF3_HUMAN
Polymorphism
2227329
A/C
L
125
M
2
UniProt
VAR_013074
A
174
T
CSF3_HUMAN
Polymorphism
2227330
A/C
A
142
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: INTERLEUKIN_6 (A:65-90,C:65-90)
2: FN3 (B:7-112,D:7-112|B:117-212,D:117-21...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTERLEUKIN_6
PS00254
Interleukin-6 / G-CSF / MGF signature.
CSF3_HUMAN
97-122
2
A:65-90
C:65-90
2
FN3
PS50853
Fibronectin type-III domain profile.
CSF3R_MOUSE
126-231
236-331
434-529
334-433
530-624
4
B:7-112
D:7-112
B:117-212
D:117-212
-
-
-
[
close PROSITE info
]
Exons
(4, 8)
Info
All Exons
Exon 1.1f (A:5-36 | C:7-36)
Exon 1.2a (A:37-72 | C:37-72)
Exon 1.2c (A:73-121 | C:73-121)
Exon 1.3c (A:122-175 | C:122-175)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1b/1.1f
2: Boundary 1.1f/1.2a
3: Boundary 1.2a/1.2c
4: Boundary 1.2c/1.3c
5: Boundary 1.3c/-
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
1.1b
ENST00000225474
1b
ENSE00001309996
chr17:
38171697-38171767
71
CSF3_HUMAN
1-14
14
0
-
-
1.1f
ENST00000225474
1f
ENSE00000950689
chr17:
38171944-38172107
164
CSF3_HUMAN
14-68
55
2
A:5-36
C:7-36
32
30
1.2a
ENST00000225474
2a
ENSE00000950690
chr17:
38172486-38172593
108
CSF3_HUMAN
69-104
36
2
A:37-72
C:37-72
36
36
1.2c
ENST00000225474
2c
ENSE00000950691
chr17:
38172738-38172884
147
CSF3_HUMAN
105-153
49
2
A:73-121
C:73-121
49
49
1.3c
ENST00000225474
3c
ENSE00001268721
chr17:
38173048-38174066
1019
CSF3_HUMAN
154-207
54
2
A:122-175
C:122-175
54
54
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1cd9a_ (A:)
1b: SCOP_d1cd9c_ (C:)
2a: SCOP_d1cd9b1 (B:1-107)
2b: SCOP_d1cd9b2 (B:108-213)
2c: SCOP_d1cd9d1 (D:2-107)
2d: SCOP_d1cd9d2 (D:108-213)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
4-helical cytokines
(168)
Superfamily
:
4-helical cytokines
(168)
Family
:
Long-chain cytokines
(46)
Protein domain
:
Granulocyte-colony stimulating factor (G-CSF)
(7)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1cd9a_
A:
1b
d1cd9c_
C:
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Fibronectin type III
(212)
Family
:
Fibronectin type III
(180)
Protein domain
:
Granulocyte colony-stimulating factor (GC-SF) receptor
(5)
Mouse (Mus musculus) [TaxId: 10090]
(4)
2a
d1cd9b1
B:1-107
2b
d1cd9b2
B:108-213
2c
d1cd9d1
D:2-107
2d
d1cd9d2
D:108-213
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1cd9C00 (C:7-175)
1b: CATH_1cd9A00 (A:5-175)
2a: CATH_1cd9D01 (D:2-108)
2b: CATH_1cd9B01 (B:1-108)
2c: CATH_1cd9B02 (B:109-213)
2d: CATH_1cd9D02 (D:109-212)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Growth Hormone; Chain: A;
(136)
Homologous Superfamily
:
[code=1.20.1250.10, no name defined]
(130)
Human (Homo sapiens)
(110)
1a
1cd9C00
C:7-175
1b
1cd9A00
A:5-175
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1cd9D01
D:2-108
2b
1cd9B01
B:1-108
2c
1cd9B02
B:109-213
2d
1cd9D02
D:109-212
[
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
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 (130 KB)
Header - Asym.Unit
Biol.Unit 1 (125 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
1CD9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help