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.
1EXZ
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (46 KB)
Biol.Unit 2 (43 KB)
Biol.Unit 3 (87 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF STEM CELL FACTOR
Authors
:
Z. Zhang, R. Zhang, A. Joachimiak, J. Schlessinger, X. Kong
Date
:
05 May 00 (Deposition) - 06 Jul 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Scf, Hormone/Growth Factor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Zhang, R. Zhang, A. Joachimiak, J. Schlessinger, X. P. Kong
Crystal Structure Of Human Stem Cell Factor: Implication For Stem Cell Factor Receptor Dimerization And Activation.
Proc. Natl. Acad. Sci. Usa V. 97 7732 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: SAMARIUM (III) ION (SMa)
2b: SAMARIUM (III) ION (SMb)
2c: SAMARIUM (III) ION (SMc)
2d: SAMARIUM (III) ION (SMd)
3a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
SM
4
Ligand/Ion
SAMARIUM (III) ION
3
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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
ASP C:454 , ASP C:458 , HOH C:946
BINDING SITE FOR RESIDUE SM C 801
2
AC2
SOFTWARE
ARG B:207 , ASP B:285 , GLU B:288 , ASP D:677
BINDING SITE FOR RESIDUE SM B 802
3
AC3
SOFTWARE
ASP B:337 , VAL B:339 , HOH B:859
BINDING SITE FOR RESIDUE SM B 803
4
AC4
SOFTWARE
ASP A:124 , ASP A:128 , PHE C:529 , VAL C:531 , SER C:533
BINDING SITE FOR RESIDUE SM C 804
5
AC5
SOFTWARE
SER B:267 , HOH B:937 , HOH B:943 , GLU C:513
BINDING SITE FOR RESIDUE CA C 805
6
AC6
SOFTWARE
ASP A:54 , ASP A:58
BINDING SITE FOR RESIDUE CA A 806
7
AC7
SOFTWARE
GLU B:288 , ASN D:681 , ASP D:685
BINDING SITE FOR RESIDUE TRS D 807
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_063237 (N611S, chain A/B/C/D, )
2: VAR_042652 (T629A, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_063237
N
36
S
SCF_HUMAN
Disease (FPHH)
---
A
B
C
D
N
11
211
411
611
S
2
UniProt
VAR_042652
T
54
A
SCF_HUMAN
Polymorphism
3741457
A
B
C
D
T
29
229
429
629
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(4, 16)
Info
All Exons
Exon 1.3 (A:4-18 | B:202-218 | C:409-418 | D...)
Exon 1.5 (A:19-39 | B:219-239 | C:419-439 | ...)
Exon 1.6 (A:40-96 | B:240-296 | C:440-496 | ...)
Exon 1.7 (A:97-139 (gaps) | B:297-341 | C:49...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.3
2: Boundary 1.3/1.5
3: Boundary 1.5/1.6
4: Boundary 1.6/1.7
5: Boundary 1.7/1.8
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
ENST00000228280
1
ENSE00000993383
chr12:
88974238-88974041
198
SCF_HUMAN
1-5
5
0
-
-
1.3
ENST00000228280
3
ENSE00000909415
chr12:
88939642-88939529
114
SCF_HUMAN
6-43
38
4
A:4-18
B:202-218
C:409-418
D:609-618
15
17
10
10
1.5
ENST00000228280
5
ENSE00000909413
chr12:
88926280-88926218
63
SCF_HUMAN
44-64
21
4
A:19-39
B:219-239
C:419-439
D:619-639
21
21
21
21
1.6
ENST00000228280
6
ENSE00000537922
chr12:
88912644-88912474
171
SCF_HUMAN
65-121
57
4
A:40-96
B:240-296
C:440-496
D:640-696
57
57
57
57
1.7
ENST00000228280
7
ENSE00000752892
chr12:
88910267-88910111
157
SCF_HUMAN
122-174
53
4
A:97-139 (gaps)
B:297-341
C:497-539
D:697-732
43
45
43
36
1.8
ENST00000228280
8
ENSE00001416325
chr12:
88909394-88909311
84
SCF_HUMAN
174-202
29
0
-
-
1.9
ENST00000228280
9
ENSE00000843426
chr12:
88900914-88900805
110
SCF_HUMAN
202-238
37
0
-
-
1.10
ENST00000228280
10
ENSE00000843425
chr12:
88900155-88900088
68
SCF_HUMAN
239-261
23
0
-
-
1.11
ENST00000228280
11
ENSE00001303130
chr12:
88899012-88898936
77
SCF_HUMAN
261-273
13
0
-
-
1.12
ENST00000228280
12
ENSE00000993382
chr12:
88890958-88886566
4393
SCF_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1exza_ (A:)
1b: SCOP_d1exzb_ (B:)
1c: SCOP_d1exzc_ (C:)
1d: SCOP_d1exzd_ (D:)
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
:
Short-chain cytokines
(78)
Protein domain
:
Stem cell factor, SCF
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1exza_
A:
1b
d1exzb_
B:
1c
d1exzc_
C:
1d
d1exzd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1exzB00 (B:202-341)
1b: CATH_1exzD00 (D:609-732)
1c: CATH_1exzA00 (A:4-139)
1d: CATH_1exzC00 (C:409-539)
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
1exzB00
B:202-341
1b
1exzD00
D:609-732
1c
1exzA00
A:4-139
1d
1exzC00
C:409-539
[
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 (93 KB)
Header - Asym.Unit
Biol.Unit 1 (46 KB)
Header - Biol.Unit 1
Biol.Unit 2 (43 KB)
Header - Biol.Unit 2
Biol.Unit 3 (87 KB)
Header - Biol.Unit 3
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
1EXZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
