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4DKD
Asym. Unit
Info
Asym.Unit (108 KB)
Biol.Unit 1 (101 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-34 BOUND TO HUMAN CSF-1R
Authors
:
X. Ma, J. F. Bazan, M. A. Starovasnik
Date
:
03 Feb 12 (Deposition) - 11 Apr 12 (Release) - 25 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dimeric Four-Helix Bundle Cytokine, Receptor Tyrosine Kinase, Glycosylation, Cytokine-Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Ma, W. Y. Lin, Y. Chen, S. Stawicki, K. Mukhyala, Y. Wu, F. Martin, J. F. Bazan, M. A. Starovasnik
Structural Basis For The Dual Recognition Of Helical Cytokines Il-34 And Csf-1 By Csf-1R.
Structure V. 20 676 2012
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:68 , GLU A:69 , VAL A:71 , PHE A:72 , ASN A:76 , ARG A:79 , VAL A:145 , NAG A:302
BINDING SITE FOR RESIDUE NAG A 301
02
AC2
SOFTWARE
TYR A:68 , GLU A:69 , LYS A:157 , NAG A:301 , BMA A:303
BINDING SITE FOR RESIDUE NAG A 302
03
AC3
SOFTWARE
NAG A:302 , HOH A:401
BINDING SITE FOR RESIDUE BMA A 303
04
AC4
SOFTWARE
GLU B:69 , VAL B:71 , PHE B:72 , ASN B:76 , ARG B:79 , NAG B:302 , HOH B:401
BINDING SITE FOR RESIDUE NAG B 301
05
AC5
SOFTWARE
TYR B:68 , GLU B:69 , LYS B:157 , NAG B:301 , BMA B:303
BINDING SITE FOR RESIDUE NAG B 302
06
AC6
SOFTWARE
TYR B:68 , NAG B:302 , HOH B:402
BINDING SITE FOR RESIDUE BMA B 303
07
AC7
SOFTWARE
ASN C:73 , HOH C:501
BINDING SITE FOR RESIDUE NAG C 401
08
AC8
SOFTWARE
ASN C:153
BINDING SITE FOR RESIDUE NAG C 402
09
AC9
SOFTWARE
ASN C:240 , PHE C:270 , GLN C:271 , ALA C:273
BINDING SITE FOR RESIDUE NAG C 403
10
BC1
SOFTWARE
ASN C:275 , SER C:290 , PHE C:292
BINDING SITE FOR RESIDUE NAG C 404
[
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SAPs(SNPs)/Variants
(4, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_042038 (V32G, chain C, )
2: VAR_033164 (E123Q, chain A/B, )
3: VAR_061290 (A245S, chain C, )
4: VAR_049718 (V279M, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_042038
V
32
G
CSF1R_HUMAN
Polymorphism
56048668
C
V
32
G
2
UniProt
VAR_033164
E
123
Q
IL34_HUMAN
Polymorphism
8046424
A/B
E
123
Q
3
UniProt
VAR_061290
A
245
S
CSF1R_HUMAN
Polymorphism
41338945
C
A
245
S
4
UniProt
VAR_049718
V
279
M
CSF1R_HUMAN
Polymorphism
3829986
C
V
279
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
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Exons
(4, 4)
Info
All Exons
Exon 1.3 (C:20-103 (gaps))
Exon 1.4 (C:103-198)
Exon 1.5 (C:198-243)
Exon 1.6a (C:244-295)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2b/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6a
5: Boundary 1.6a/1.7
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
ENST00000286301
1
ENSE00000841168
chr5:
149492935-149492824
112
CSF1R_HUMAN
-
0
0
-
-
1.2b
ENST00000286301
2b
ENSE00001366842
chr5:
149466170-149465942
229
CSF1R_HUMAN
1-17
17
0
-
-
1.3
ENST00000286301
3
ENSE00001023095
chr5:
149460587-149460330
258
CSF1R_HUMAN
17-103
87
1
C:20-103 (gaps)
84
1.4
ENST00000286301
4
ENSE00001023084
chr5:
149459899-149459615
285
CSF1R_HUMAN
103-198
96
1
C:103-198
96
1.5
ENST00000286301
5
ENSE00001023099
chr5:
149457811-149457675
137
CSF1R_HUMAN
198-243
46
1
C:198-243
46
1.6a
ENST00000286301
6a
ENSE00001023081
chr5:
149456998-149456839
160
CSF1R_HUMAN
244-297
54
1
C:244-295
52
1.7
ENST00000286301
7
ENSE00001023101
chr5:
149453056-149452864
193
CSF1R_HUMAN
297-361
65
0
-
-
1.8
ENST00000286301
8
ENSE00001023092
chr5:
149450134-149450019
116
CSF1R_HUMAN
361-400
40
0
-
-
1.9
ENST00000286301
9
ENSE00001023097
chr5:
149449865-149449745
121
CSF1R_HUMAN
400-440
41
0
-
-
1.10
ENST00000286301
10
ENSE00001023094
chr5:
149449626-149449436
191
CSF1R_HUMAN
440-504
65
0
-
-
1.11
ENST00000286301
11
ENSE00001023090
chr5:
149447893-149447778
116
CSF1R_HUMAN
504-542
39
0
-
-
1.13a
ENST00000286301
13a
ENSE00001023078
chr5:
149441412-149441286
127
CSF1R_HUMAN
543-585
43
0
-
-
1.13d
ENST00000286301
13d
ENSE00001023098
chr5:
149441158-149441054
105
CSF1R_HUMAN
585-620
36
0
-
-
1.14
ENST00000286301
14
ENSE00001023088
chr5:
149440535-149440425
111
CSF1R_HUMAN
620-657
38
0
-
-
1.15b
ENST00000286301
15b
ENSE00001023096
chr5:
149439425-149439263
163
CSF1R_HUMAN
657-711
55
0
-
-
1.17
ENST00000286301
17
ENSE00001023083
chr5:
149437155-149437067
89
CSF1R_HUMAN
711-741
31
0
-
-
1.18
ENST00000286301
18
ENSE00001023077
chr5:
149436947-149436850
98
CSF1R_HUMAN
741-773
33
0
-
-
1.19
ENST00000286301
19
ENSE00001023079
chr5:
149435904-149435782
123
CSF1R_HUMAN
774-814
41
0
-
-
1.20
ENST00000286301
20
ENSE00001684899
chr5:
149435700-149435589
112
CSF1R_HUMAN
815-852
38
0
-
-
1.21
ENST00000286301
21
ENSE00001023100
chr5:
149434899-149434800
100
CSF1R_HUMAN
852-885
34
0
-
-
1.22b
ENST00000286301
22b
ENSE00001023085
chr5:
149433993-149433885
109
CSF1R_HUMAN
885-921
37
0
-
-
1.23c
ENST00000286301
23c
ENSE00001083274
chr5:
149433787-149432854
934
CSF1R_HUMAN
922-972
51
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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