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.
3L5H
Asym. Unit
Info
Asym.Unit (107 KB)
Biol.Unit 1 (96 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 FULL ECTODOMAIN OF HUMAN GP130: NEW INSIGHTS INTO THE MOLECULAR ASSEMBLY OF RECEPTOR COMPLEXES
Authors
:
Y. Xu, T. P. J. Garrett, J. G. Zhang
Date
:
21 Dec 09 (Deposition) - 19 May 10 (Release) - 05 Apr 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Ig-Like, Fniii, Cell Membrane, Disulfide Bond, Glycoprotein, Immunoglobulin Domain, Membrane, Phosphoprotein, 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
]
Hetero Components
(5, 22)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
2a: ALPHA-L-FUCOSE (FUCa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
5
Ligand/Ion
BETA-D-MANNOSE
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:121
BINDING SITE FOR RESIDUE SO4 A 1
02
AC2
SOFTWARE
ARG A:276
BINDING SITE FOR RESIDUE SO4 A 591
03
AC3
SOFTWARE
ARG A:373
BINDING SITE FOR RESIDUE SO4 A 592
04
AC4
SOFTWARE
HIS A:204 , ASN A:205 , NAG A:594
BINDING SITE FOR RESIDUE NAG A 593
05
AC5
SOFTWARE
NAG A:593
BINDING SITE FOR RESIDUE NAG A 594
06
AC6
SOFTWARE
ASN A:135 , NAG A:596
BINDING SITE FOR RESIDUE NDG A 595
07
AC7
SOFTWARE
NDG A:595 , BMA A:597
BINDING SITE FOR RESIDUE NAG A 596
08
AC8
SOFTWARE
NAG A:596 , BMA A:598
BINDING SITE FOR RESIDUE BMA A 597
09
AC9
SOFTWARE
BMA A:597
BINDING SITE FOR RESIDUE BMA A 598
10
BC1
SOFTWARE
ASN A:61 , THR A:63 , NAG A:600
BINDING SITE FOR RESIDUE NAG A 599
11
BC2
SOFTWARE
NAG A:599
BINDING SITE FOR RESIDUE NAG A 600
12
BC3
SOFTWARE
LEU A:342 , ASN A:361 , NAG A:602
BINDING SITE FOR RESIDUE NAG A 601
13
BC4
SOFTWARE
ILE A:341 , NAG A:601 , BMA A:603
BINDING SITE FOR RESIDUE NAG A 602
14
BC5
SOFTWARE
NAG A:602
BINDING SITE FOR RESIDUE BMA A 603
15
BC6
SOFTWARE
ARG A:530 , ASN A:531 , ASP A:575 , NAG A:607
BINDING SITE FOR RESIDUE NAG A 606
16
BC7
SOFTWARE
ASP A:575 , GLU A:576 , NAG A:606 , BMA A:608
BINDING SITE FOR RESIDUE NAG A 607
17
BC8
SOFTWARE
NAG A:607 , BMA A:609
BINDING SITE FOR RESIDUE BMA A 608
18
BC9
SOFTWARE
BMA A:608
BINDING SITE FOR RESIDUE BMA A 609
19
CC1
SOFTWARE
GLU A:345 , ASN A:357 , FUC A:605
BINDING SITE FOR RESIDUE NAG A 604
20
CC2
SOFTWARE
NAG A:604
BINDING SITE FOR RESIDUE FUC A 605
21
CC3
SOFTWARE
ASN A:21 , NAG A:611
BINDING SITE FOR RESIDUE NAG A 610
22
CC4
SOFTWARE
NAG A:610
BINDING SITE FOR RESIDUE NAG A 611
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_047783 (G126R, chain A, )
2: VAR_047784 (L375V, chain A, )
3: VAR_036165 (T393I, chain A, )
4: VAR_IL6RB_HUMAN_CCDS3971_1_01 (T393I, chain A, )
5: VAR_047785 (I432T, chain A, )
6: VAR_047786 (V477I, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_047783
G
148
R
IL6RB_HUMAN
Polymorphism
2228044
A
G
126
R
2
UniProt
VAR_047784
L
397
V
IL6RB_HUMAN
Polymorphism
2228043
A
L
375
V
3
UniProt
VAR_036165
T
415
I
IL6RB_HUMAN
Unclassified
---
A
T
393
I
4
CancerSNP
VAR_IL6RB_HUMAN_CCDS3971_1_01
*
T
415
I
IL6RB_HUMAN
Disease (Colorectal cancer)
---
A
T
393
I
5
UniProt
VAR_047785
I
454
T
IL6RB_HUMAN
Polymorphism
2228046
A
I
432
T
6
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, 5)
Info
All PROSITE Patterns/Profiles
1: FN3 (A:202-302|A:496-590|A:404-495|A:30...)
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
4
A:202-302
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
(11, 11)
Info
All Exons
Exon 1.4b (A:2-102 (gaps))
Exon 1.5 (A:102-142)
Exon 1.6b (A:142-198)
Exon 1.7 (A:198-249)
Exon 1.8a (A:250-303)
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
01: Boundary 1.3c/1.4b
02: Boundary 1.4b/1.5
03: Boundary 1.5/1.6b
04: Boundary 1.6b/1.7
05: Boundary 1.7/1.8a
06: Boundary 1.8a/1.10
07: Boundary 1.10/1.11a
08: Boundary 1.11a/1.12
09: Boundary 1.12/1.13
10: Boundary 1.13/1.14
11: Boundary 1.14/1.15a
12: 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
1
A:2-102 (gaps)
101
1.5
ENST00000381298
5
ENSE00000914153
chr5:
55264224-55264104
121
IL6RB_HUMAN
124-164
41
1
A:102-142
41
1.6b
ENST00000381298
6b
ENSE00000914150
chr5:
55260140-55259974
167
IL6RB_HUMAN
164-220
57
1
A:142-198
57
1.7
ENST00000381298
7
ENSE00000914147
chr5:
55259334-55259180
155
IL6RB_HUMAN
220-271
52
1
A:198-249
52
1.8a
ENST00000381298
8a
ENSE00001006585
chr5:
55256389-55256230
160
IL6RB_HUMAN
272-325
54
1
A:250-303
54
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
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_IL6Ra_bind_3l5hA01 (A:106-195)
2a: PFAM_fn3_3l5hA02 (A:496-583)
2b: PFAM_fn3_3l5hA03 (A:496-583)
3a: PFAM_Lep_receptor_Ig_3l5hA04 (A:2-92)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
E-set
(290)
Family
:
IL6Ra-bind
(3)
Homo sapiens (Human)
(3)
1a
IL6Ra-bind-3l5hA01
A:106-195
Family
:
fn3
(66)
Homo sapiens (Human)
(52)
2a
fn3-3l5hA02
A:496-583
2b
fn3-3l5hA03
A:496-583
Clan
:
Ig
(577)
Family
:
Lep_receptor_Ig
(2)
Homo sapiens (Human)
(2)
3a
Lep_receptor_Ig-3l5hA04
A:2-92
[
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 (107 KB)
Header - Asym.Unit
Biol.Unit 1 (96 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
3L5H
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help