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3L5I
Asym. Unit
Info
Asym.Unit (105 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FNIII DOMAINS OF HUMAN GP130 (DOMAINS 4-6)
Authors
:
N. J. Kershaw, J. -G. Zhang, T. P. J. Garrett, P. E. Czabotar
Date
:
22 Dec 09 (Deposition) - 12 May 10 (Release) - 05 Apr 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Cytokine Receptor, Fibronectin Type Iii Domain, Cell Membrane, Disulfide Bond, Immunoglobulin Domain, Membrane, Receptor, Secreted, Transmembrane, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Xu, N. J. Kershaw, C. S. Luo, P. Soo, M. J. Pocock, P. E. Czabotar, D. J. Hilton, N. A. Nicola, T. P. Garrett, J. G. Zhang
Crystal Structure Of The Entire Ectodomain Of Gp130: Insights Into The Molecular Assembly Of The Tall Cytokine Receptor Complexes.
J. Biol. Chem. V. 285 21214 2010
[
close entry info
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
3
Ligand/Ion
CHLORIDE ION
2
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
3
MSE
4
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(20, 20)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
EDO A:10 , HOH A:53 , THR A:366 , VAL A:437 , TYR A:470 , HOH A:612
BINDING SITE FOR RESIDUE EDO A 1
02
AC2
SOFTWARE
HOH A:55 , HOH A:112 , PRO A:412 , ALA A:490 , TYR A:491 , GLN A:494 , PHE A:528
BINDING SITE FOR RESIDUE EDO A 2
03
AC3
SOFTWARE
PHE A:535 , ARG A:537 , GLU A:543 , MSE A:567 , VAL A:568 , ARG A:569 , GLU A:583
BINDING SITE FOR RESIDUE EDO A 3
04
AC4
SOFTWARE
HOH A:51 , HOH A:295 , PHE A:399 , ALA A:401 , THR A:402 , TYR A:478 , ASP A:480 , PRO A:482 , GLY A:483
BINDING SITE FOR RESIDUE EDO A 4
05
AC5
SOFTWARE
ARG A:569 , TYR A:573 , ASP A:580
BINDING SITE FOR RESIDUE EDO A 5
06
AC6
SOFTWARE
GLU A:426 , VAL A:428 , GLY A:453
BINDING SITE FOR RESIDUE EDO A 6
07
AC7
SOFTWARE
HOH A:125 , HIS A:403 , PRO A:404 , ASN A:542 , THR A:544
BINDING SITE FOR RESIDUE EDO A 7
08
AC8
SOFTWARE
GLU A:434 , LEU A:471 , THR A:473
BINDING SITE FOR RESIDUE EDO A 8
09
AC9
SOFTWARE
VAL A:328 , GLU A:434 , THR A:446 , TRP A:448 , HOH A:638
BINDING SITE FOR RESIDUE EDO A 9
10
BC1
SOFTWARE
EDO A:1 , HOH A:72 , ASN A:368 , TRP A:435 , VAL A:437 , ILE A:445 , ASP A:447
BINDING SITE FOR RESIDUE EDO A 10
11
BC2
SOFTWARE
HOH A:92 , ILE A:341 , ASN A:361
BINDING SITE FOR RESIDUE EDO A 11
12
BC3
SOFTWARE
HOH A:292 , TRP A:311 , TYR A:312
BINDING SITE FOR RESIDUE EDO A 12
13
BC4
SOFTWARE
PRO A:316 , SER A:317 , ALA A:362 , THR A:363
BINDING SITE FOR RESIDUE EDO A 13
14
BC5
SOFTWARE
LYS A:510 , ASN A:511 , GLU A:512
BINDING SITE FOR RESIDUE CL A 591
15
BC6
SOFTWARE
MSE A:416 , LEU A:417 , LEU A:460 , GLY A:462 , LEU A:464 , HOH A:648
BINDING SITE FOR RESIDUE EDO A 14
16
BC7
SOFTWARE
ILE A:488 , LYS A:489
BINDING SITE FOR RESIDUE CL A 592
17
BC8
SOFTWARE
ARG A:457 , GLY A:509 , GLU A:512 , VAL A:514 , THR A:556
BINDING SITE FOR RESIDUE EDO A 15
18
BC9
SOFTWARE
THR A:402 , SER A:559 , LEU A:560 , THR A:561 , TYR A:566
BINDING SITE FOR RESIDUE EDO A 16
19
CC1
SOFTWARE
SER A:309 , GLN A:450 , ARG A:461 , HOH A:606
BINDING SITE FOR RESIDUE CL A 593
20
CC2
SOFTWARE
TYR A:555 , THR A:556
BINDING SITE FOR RESIDUE EDO A 17
[
close Site info
]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_047784 (L375V, chain A, )
2: VAR_036165 (T393I, chain A, )
3: VAR_IL6RB_HUMAN_CCDS3971_1_01 (T393I, chain A, )
4: VAR_047785 (I432T, chain A, )
5: VAR_047786 (V477I, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_047784
L
397
V
IL6RB_HUMAN
Polymorphism
2228043
A
L
375
V
2
UniProt
VAR_036165
T
415
I
IL6RB_HUMAN
Unclassified
---
A
T
393
I
3
CancerSNP
VAR_IL6RB_HUMAN_CCDS3971_1_01
*
T
415
I
IL6RB_HUMAN
Disease (Colorectal cancer)
---
A
T
393
I
4
UniProt
VAR_047785
I
454
T
IL6RB_HUMAN
Polymorphism
2228046
A
I
432
T
5
UniProt
VAR_047786
V
499
I
IL6RB_HUMAN
Polymorphism
34417936
A
V
477
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: FN3 (-|A:496-590|A:404-495|A:307-402)
2: HEMATOPO_REC_L_F2 (A:382-435)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FN3
PS50853
Fibronectin type-III domain profile.
IL6RB_HUMAN
224-324
518-613
426-517
329-424
3
-
A:496-590
A:404-495
A:307-402
2
HEMATOPO_REC_L_F2
PS01353
Long hematopoietin receptor, gp130 family signature.
IL6RB_HUMAN
404-457
1
A:382-435
[
close PROSITE info
]
Exons
(7, 7)
Info
All Exons
Exon 1.8a (A:301-303)
Exon 1.10 (A:303-330)
Exon 1.11a (A:331-401)
Exon 1.12 (A:401-462)
Exon 1.13 (A:462-496)
Exon 1.14 (A:496-545)
Exon 1.15a (A:545-590)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.7/1.8a
2: Boundary 1.8a/1.10
3: Boundary 1.10/1.11a
4: Boundary 1.11a/1.12
5: Boundary 1.12/1.13
6: Boundary 1.13/1.14
7: Boundary 1.14/1.15a
8: Boundary 1.15a/1.17d
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
ENST00000381298
1a
ENSE00001488125
chr5:
55290772-55290612
161
IL6RB_HUMAN
-
0
0
-
-
1.2a
ENST00000381298
2a
ENSE00001488122
chr5:
55278639-55278552
88
IL6RB_HUMAN
-
0
0
-
-
1.3c
ENST00000381298
3c
ENSE00002172585
chr5:
55272121-55272043
79
IL6RB_HUMAN
1-22
22
0
-
-
1.4b
ENST00000381298
4b
ENSE00000914155
chr5:
55265683-55265378
306
IL6RB_HUMAN
22-124
103
0
-
-
1.5
ENST00000381298
5
ENSE00000914153
chr5:
55264224-55264104
121
IL6RB_HUMAN
124-164
41
0
-
-
1.6b
ENST00000381298
6b
ENSE00000914150
chr5:
55260140-55259974
167
IL6RB_HUMAN
164-220
57
0
-
-
1.7
ENST00000381298
7
ENSE00000914147
chr5:
55259334-55259180
155
IL6RB_HUMAN
220-271
52
0
-
-
1.8a
ENST00000381298
8a
ENSE00001006585
chr5:
55256389-55256230
160
IL6RB_HUMAN
272-325
54
1
A:301-303
3
1.10
ENST00000381298
10
ENSE00000914138
chr5:
55253119-55253037
83
IL6RB_HUMAN
325-352
28
1
A:303-330
28
1.11a
ENST00000381298
11a
ENSE00001745568
chr5:
55252063-55251853
211
IL6RB_HUMAN
353-423
71
1
A:331-401
71
1.12
ENST00000381298
12
ENSE00001685217
chr5:
55250820-55250638
183
IL6RB_HUMAN
423-484
62
1
A:401-462
62
1.13
ENST00000381298
13
ENSE00001781723
chr5:
55248179-55248078
102
IL6RB_HUMAN
484-518
35
1
A:462-496
35
1.14
ENST00000381298
14
ENSE00001750732
chr5:
55247903-55247757
147
IL6RB_HUMAN
518-567
50
1
A:496-545
50
1.15a
ENST00000381298
15a
ENSE00001667221
chr5:
55247432-55247292
141
IL6RB_HUMAN
567-614
48
1
A:545-590
46
1.17d
ENST00000381298
17d
ENSE00001743622
chr5:
55243417-55243321
97
IL6RB_HUMAN
614-646
33
0
-
-
1.18
ENST00000381298
18
ENSE00001611906
chr5:
55238579-55238498
82
IL6RB_HUMAN
646-673
28
0
-
-
1.19e
ENST00000381298
19e
ENSE00001488109
chr5:
55237647-55230923
6725
IL6RB_HUMAN
674-918
245
0
-
-
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Asymmetric Unit 1
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