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.
2EC8
Asym. Unit
Info
Asym.Unit (82 KB)
Biol.Unit 1 (74 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 THE EXCTRACELLULAR DOMAIN OF THE RECEPTOR TYROSINE KINASE, KIT
Authors
:
S. Yuzawa, Y. Opatowsky, Z. Zhang, V. Mandiyan, I. Lax, J. Schlessinger
Date
:
11 Feb 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Glycoprotein, Receptor Tyrosine Kinase, Growth Factor Cytokine, Dimerization, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Yuzawa, Y. Opatowsky, Z. Zhang, V. Mandiyan, I. Lax, J. Schlessinge
Structural Basis For Activation Of The Receptor Tyrosine Kinase Kit By Stem Cell Factor
Cell(Cambridge, Mass. ) V. 130 323 2007
[
close entry info
]
Hetero Components
(1, 5)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:127 , GLU A:128 , ASP A:129 , ASN A:130 , ALA A:207
BINDING SITE FOR RESIDUE NAG A 700
2
AC2
SOFTWARE
PRO A:41 , GLY A:42 , LYS A:43 , TYR A:291 , ASN A:293
BINDING SITE FOR RESIDUE NAG A 750
3
AC3
SOFTWARE
TYR A:291 , ASN A:300 , GLU A:368
BINDING SITE FOR RESIDUE NAG A 800
4
AC4
SOFTWARE
SER A:365 , ASN A:367 , SER A:369
BINDING SITE FOR RESIDUE NAG A 850
5
AC5
SOFTWARE
ASP A:189 , ASN A:320
BINDING SITE FOR RESIDUE NAG A 900
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.1a (A:11-18)
Exon 1.2a (A:33-113)
Exon 1.3 (A:113-207 (gaps))
Exon 1.4 (A:207-252)
Exon 1.5 (A:253-309)
Exon 1.6 (A:309-372)
Exon 1.7 (A:372-411)
Exon 1.8 (A:411-443)
Exon 1.9b (A:454-508 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2a
03: Boundary 1.2a/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9b
10: Boundary 1.9b/1.10
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
1.1a
ENST00000288135
1a
ENSE00001905199
chr4:
55524085-55524248
164
KIT_HUMAN
1-23
23
1
A:11-18
8
1.2a
ENST00000288135
2a
ENSE00001032350
chr4:
55561678-55561947
270
KIT_HUMAN
23-113
91
1
A:33-113
81
1.3
ENST00000288135
3
ENSE00001074448
chr4:
55564450-55564731
282
KIT_HUMAN
113-207
95
1
A:113-207 (gaps)
95
1.4
ENST00000288135
4
ENSE00001121859
chr4:
55565796-55565932
137
KIT_HUMAN
207-252
46
1
A:207-252
46
1.5
ENST00000288135
5
ENSE00001074426
chr4:
55569890-55570058
169
KIT_HUMAN
253-309
57
1
A:253-309
57
1.6
ENST00000288135
6
ENSE00001074418
chr4:
55573264-55573453
190
KIT_HUMAN
309-372
64
1
A:309-372
64
1.7
ENST00000288135
7
ENSE00001074452
chr4:
55575590-55575705
116
KIT_HUMAN
372-411
40
1
A:372-411
40
1.8
ENST00000288135
8
ENSE00001074431
chr4:
55589750-55589864
115
KIT_HUMAN
411-449
39
1
A:411-443
33
1.9b
ENST00000288135
9b
ENSE00001074423
chr4:
55592023-55592216
194
KIT_HUMAN
449-514
66
1
A:454-508 (gaps)
55
1.10
ENST00000288135
10
ENSE00001074410
chr4:
55593384-55593490
107
KIT_HUMAN
514-549
36
0
-
-
1.11
ENST00000288135
11
ENSE00001074417
chr4:
55593582-55593708
127
KIT_HUMAN
550-592
43
0
-
-
1.12
ENST00000288135
12
ENSE00001074438
chr4:
55593989-55594093
105
KIT_HUMAN
592-627
36
0
-
-
1.13
ENST00000288135
13
ENSE00001074408
chr4:
55594177-55594287
111
KIT_HUMAN
627-664
38
0
-
-
1.14b
ENST00000288135
14b
ENSE00001074445
chr4:
55595501-55595651
151
KIT_HUMAN
664-714
51
0
-
-
1.15
ENST00000288135
15
ENSE00001074450
chr4:
55597494-55597585
92
KIT_HUMAN
714-745
32
0
-
-
1.16
ENST00000288135
16
ENSE00001074441
chr4:
55598037-55598164
128
KIT_HUMAN
745-787
43
0
-
-
1.17a
ENST00000288135
17a
ENSE00001074435
chr4:
55599236-55599358
123
KIT_HUMAN
788-828
41
0
-
-
1.18
ENST00000288135
18
ENSE00001074442
chr4:
55602664-55602775
112
KIT_HUMAN
829-866
38
0
-
-
1.19
ENST00000288135
19
ENSE00001224349
chr4:
55602887-55602986
100
KIT_HUMAN
866-899
34
0
-
-
1.20
ENST00000288135
20
ENSE00001074415
chr4:
55603341-55603446
106
KIT_HUMAN
899-934
36
0
-
-
1.21b
ENST00000288135
21b
ENSE00001898693
chr4:
55604595-55606881
2287
KIT_HUMAN
935-976
42
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_2ec8A03 (A:208-311)
1b: CATH_2ec8A04 (A:312-411)
1c: CATH_2ec8A01 (A:11-116)
1d: CATH_2ec8A02 (A:117-207)
1e: CATH_2ec8A05 (A:412-508)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
2ec8A03
A:208-311
1b
2ec8A04
A:312-411
1c
2ec8A01
A:11-116
1d
2ec8A02
A:117-207
1e
2ec8A05
A:412-508
[
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 (82 KB)
Header - Asym.Unit
Biol.Unit 1 (74 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
2EC8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
