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2E9W
Asym. Unit
Info
Asym.Unit (197 KB)
Biol.Unit 1 (190 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF KIT IN COMPLEX WITH STEM CELL FACTOR (SCF)
Authors
:
S. Yuzawa, Y. Opatowsky, Z. Zhang, V. Mandiyan, I. Lax, J. Schlessinger
Date
:
27 Jan 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Glycoprotein, Receptor Tyrosine Kinase, Growth Factor Cytokine, Dimerization, Transferase-Hormone Complex
(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
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Hetero Components
(1, 6)
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)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:283
BINDING SITE FOR RESIDUE NAG A 700
2
AC2
SOFTWARE
TYR A:291 , ASN A:300
BINDING SITE FOR RESIDUE NAG A 750
3
AC3
SOFTWARE
ASN A:352
BINDING SITE FOR RESIDUE NAG A 800
4
AC4
SOFTWARE
TYR B:291 , ASN B:293
BINDING SITE FOR RESIDUE NAG B 850
5
AC5
SOFTWARE
ALA B:299 , ASN B:300
BINDING SITE FOR RESIDUE NAG B 900
6
AC6
SOFTWARE
ASN B:352
BINDING SITE FOR RESIDUE NAG B 950
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_063237 (N11S, chain C/D, )
2: VAR_042652 (T29A, chain 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)
---
C/D
N
11
S
2
UniProt
VAR_042652
T
54
A
SCF_HUMAN
Polymorphism
3741457
C/D
T
29
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(12, 24)
Info
All Exons
Exon 1.3 (C:2-18 | D:3-18)
Exon 1.5 (C:19-39 | D:19-39)
Exon 1.6 (C:40-95 | D:40-96)
Exon 1.7 (C:100-140 (gaps) | D:97-130)
Exon 2.2a (A:33-113 | B:33-113)
Exon 2.3 (A:113-207 | B:113-207)
Exon 2.4 (A:207-252 | B:207-252)
Exon 2.5 (A:253-309 | B:253-309)
Exon 2.6 (A:309-372 | B:309-372 (gaps))
Exon 2.7 (A:372-411 | B:372-411)
Exon 2.8 (A:411-445 | B:411-445)
Exon 2.9b (A:450-507 (gaps) | B:450-507)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1/1.3
02: Boundary 1.3/1.5
03: Boundary 1.5/1.6
04: Boundary 1.6/1.7
05: Boundary 1.7/1.8
06: Boundary 2.1a/2.2a
07: Boundary 2.2a/2.3
08: Boundary 2.3/2.4
09: Boundary 2.4/2.5
10: Boundary 2.5/2.6
11: Boundary 2.6/2.7
12: Boundary 2.7/2.8
13: Boundary 2.8/2.9b
14: Boundary 2.9b/2.10
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
1.1
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
2
C:2-18
D:3-18
17
16
1.5
ENST00000228280
5
ENSE00000909413
chr12:
88926280-88926218
63
SCF_HUMAN
44-64
21
2
C:19-39
D:19-39
21
21
1.6
ENST00000228280
6
ENSE00000537922
chr12:
88912644-88912474
171
SCF_HUMAN
65-121
57
2
C:40-95
D:40-96
56
57
1.7
ENST00000228280
7
ENSE00000752892
chr12:
88910267-88910111
157
SCF_HUMAN
122-174
53
2
C:100-140 (gaps)
D:97-130
41
34
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
-
-
2.1a
ENST00000288135
1a
ENSE00001905199
chr4:
55524085-55524248
164
KIT_HUMAN
1-23
23
0
-
-
2.2a
ENST00000288135
2a
ENSE00001032350
chr4:
55561678-55561947
270
KIT_HUMAN
23-113
91
2
A:33-113
B:33-113
81
81
2.3
ENST00000288135
3
ENSE00001074448
chr4:
55564450-55564731
282
KIT_HUMAN
113-207
95
2
A:113-207
B:113-207
95
95
2.4
ENST00000288135
4
ENSE00001121859
chr4:
55565796-55565932
137
KIT_HUMAN
207-252
46
2
A:207-252
B:207-252
46
46
2.5
ENST00000288135
5
ENSE00001074426
chr4:
55569890-55570058
169
KIT_HUMAN
253-309
57
2
A:253-309
B:253-309
57
57
2.6
ENST00000288135
6
ENSE00001074418
chr4:
55573264-55573453
190
KIT_HUMAN
309-372
64
2
A:309-372
B:309-372 (gaps)
64
64
2.7
ENST00000288135
7
ENSE00001074452
chr4:
55575590-55575705
116
KIT_HUMAN
372-411
40
2
A:372-411
B:372-411
40
40
2.8
ENST00000288135
8
ENSE00001074431
chr4:
55589750-55589864
115
KIT_HUMAN
411-449
39
2
A:411-445
B:411-445
35
35
2.9b
ENST00000288135
9b
ENSE00001074423
chr4:
55592023-55592216
194
KIT_HUMAN
449-514
66
2
A:450-507 (gaps)
B:450-507
58
58
2.10
ENST00000288135
10
ENSE00001074410
chr4:
55593384-55593490
107
KIT_HUMAN
514-549
36
0
-
-
2.11
ENST00000288135
11
ENSE00001074417
chr4:
55593582-55593708
127
KIT_HUMAN
550-592
43
0
-
-
2.12
ENST00000288135
12
ENSE00001074438
chr4:
55593989-55594093
105
KIT_HUMAN
592-627
36
0
-
-
2.13
ENST00000288135
13
ENSE00001074408
chr4:
55594177-55594287
111
KIT_HUMAN
627-664
38
0
-
-
2.14b
ENST00000288135
14b
ENSE00001074445
chr4:
55595501-55595651
151
KIT_HUMAN
664-714
51
0
-
-
2.15
ENST00000288135
15
ENSE00001074450
chr4:
55597494-55597585
92
KIT_HUMAN
714-745
32
0
-
-
2.16
ENST00000288135
16
ENSE00001074441
chr4:
55598037-55598164
128
KIT_HUMAN
745-787
43
0
-
-
2.17a
ENST00000288135
17a
ENSE00001074435
chr4:
55599236-55599358
123
KIT_HUMAN
788-828
41
0
-
-
2.18
ENST00000288135
18
ENSE00001074442
chr4:
55602664-55602775
112
KIT_HUMAN
829-866
38
0
-
-
2.19
ENST00000288135
19
ENSE00001224349
chr4:
55602887-55602986
100
KIT_HUMAN
866-899
34
0
-
-
2.20
ENST00000288135
20
ENSE00001074415
chr4:
55603341-55603446
106
KIT_HUMAN
899-934
36
0
-
-
2.21b
ENST00000288135
21b
ENSE00001898693
chr4:
55604595-55606881
2287
KIT_HUMAN
935-976
42
0
-
-
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2e9wc1 (C:2-140)
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Folds
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)
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
d2e9wc1
C:2-140
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2e9wC00 (C:2-140)
1b: CATH_2e9wD00 (D:3-130)
2a: CATH_2e9wA03 (A:208-310)
2b: CATH_2e9wB03 (B:208-310)
2c: CATH_2e9wA04 (A:311-412)
2d: CATH_2e9wB04 (B:311-412)
2e: CATH_2e9wA02 (A:117-207)
2f: CATH_2e9wB02 (B:117-207)
2g: CATH_2e9wB05 (B:413-507)
2h: CATH_2e9wA05 (A:413-507)
2i: CATH_2e9wA01 (A:33-116)
2j: CATH_2e9wB01 (B:33-116)
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)
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)
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)
(
)
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(
)
(
)
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
2e9wC00
C:2-140
1b
2e9wD00
D:3-130
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2e9wA03
A:208-310
2b
2e9wB03
B:208-310
2c
2e9wA04
A:311-412
2d
2e9wB04
B:311-412
2e
2e9wA02
A:117-207
2f
2e9wB02
B:117-207
2g
2e9wB05
B:413-507
2h
2e9wA05
A:413-507
2i
2e9wA01
A:33-116
2j
2e9wB01
B:33-116
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (197 KB)
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