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.
1Y6K
Asym. Unit
Info
Asym.Unit (64 KB)
Biol.Unit 1 (117 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 HUMAN IL-10 COMPLEXED WITH THE SOLUBLE IL-10R1 CHAIN
Authors
:
S. I. Yoon, B. C. Jones, K. Josepson, N. J. Logsdon, M. R. Walter
Date
:
06 Dec 04 (Deposition) - 20 Dec 05 (Release) - 30 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.52
Chains
:
Asym. Unit : L,R
Biol. Unit 1: L,R (2x)
Keywords
:
Helix Bundle, Receptor Complex, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. I. Yoon, B. C. Jones, N. J. Logsdon, M. R. Walter
Same Structure, Different Function Crystal Structure Of The Epstein-Barr Virus Il-10 Bound To The Soluble Il-10R1 Chain.
Structure V. 13 551 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(11, 11)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_016294 (L40V, chain R, )
02: VAR_071663 (W48R, chain R, )
03: VAR_063542 (T63I, chain R, )
04: VAR_071664 (Y70C, chain R, )
05: VAR_071665 (R80W, chain R, )
06: VAR_016295 (V92I, chain R, )
07: VAR_071666 (R96H, chain R, )
08: VAR_063543 (G120R, chain R, )
09: VAR_016296 (S138G, chain R, )
10: VAR_016297 (R191Q, chain R, )
11: VAR_020004 (I203V, chain R, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_016294
L
61
V
I10R1_HUMAN
Polymorphism
4252250
R
L
40
V
02
UniProt
VAR_071663
W
69
R
I10R1_HUMAN
Disease (IBD28)
---
R
W
48
R
03
UniProt
VAR_063542
T
84
I
I10R1_HUMAN
Disease (IBD28)
---
R
T
63
I
04
UniProt
VAR_071664
Y
91
C
I10R1_HUMAN
Disease (IBD28)
---
R
Y
70
C
05
UniProt
VAR_071665
R
101
W
I10R1_HUMAN
Disease (IBD28)
---
R
R
80
W
06
UniProt
VAR_016295
V
113
I
I10R1_HUMAN
Polymorphism
4252303
R
V
92
I
07
UniProt
VAR_071666
R
117
H
I10R1_HUMAN
Disease (IBD28)
---
R
R
96
H
08
UniProt
VAR_063543
G
141
R
I10R1_HUMAN
Disease (IBD28)
---
R
G
120
R
09
UniProt
VAR_016296
S
159
G
I10R1_HUMAN
Polymorphism
3135932
R
S
138
G
10
UniProt
VAR_016297
R
212
Q
I10R1_HUMAN
Polymorphism
4252273
R
R
191
Q
11
UniProt
VAR_020004
I
224
V
I10R1_HUMAN
Polymorphism
2228055
R
I
203
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: INTERLEUKIN_10 (L:57-77)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTERLEUKIN_10
PS00520
Interleukin-10 family signature.
IL10_HUMAN
75-95
1
L:57-77
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.1a (R:2-2)
Exon 1.1i (R:2-42)
Exon 1.2b (R:42-102)
Exon 1.3c (R:102-158)
Exon 1.4a (R:159-206)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.1i
3: Boundary 1.1i/1.2b
4: Boundary 1.2b/1.3c
5: Boundary 1.3c/1.4a
6: Boundary 1.4a/1.5b
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
ENST00000227752
1a
ENSE00002150184
chr11:
117857063-117857249
187
I10R1_HUMAN
1-23
23
1
R:2-2
1
1.1i
ENST00000227752
1i
ENSE00001053160
chr11:
117859097-117859217
121
I10R1_HUMAN
23-63
41
1
R:2-42
41
1.2b
ENST00000227752
2b
ENSE00000795930
chr11:
117860157-117860335
179
I10R1_HUMAN
63-123
61
1
R:42-102
61
1.3c
ENST00000227752
3c
ENSE00001053158
chr11:
117863956-117864125
170
I10R1_HUMAN
123-179
57
1
R:102-158
57
1.4a
ENST00000227752
4a
ENSE00001053155
chr11:
117864714-117864864
151
I10R1_HUMAN
180-230
51
1
R:159-206
48
1.5b
ENST00000227752
5b
ENSE00001053157
chr11:
117866304-117866425
122
I10R1_HUMAN
230-270
41
0
-
-
1.6g
ENST00000227752
6g
ENSE00002200423
chr11:
117869430-117872194
2765
I10R1_HUMAN
271-578
308
0
-
-
[
close EXON info
]
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1y6kl_ (L:)
2a: SCOP_d1y6kr1 (R:2-100)
2b: SCOP_d1y6kr2 (R:101-206)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
4-helical cytokines
(168)
Superfamily
:
4-helical cytokines
(168)
Family
:
Interferons/interleukin-10 (IL-10)
(41)
Protein domain
:
Interleukin-10 (cytokine synthesis inhibitory factor, CSIF)
(10)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1y6kl_
L:
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Fibronectin type III
(212)
Family
:
Fibronectin type III
(180)
Protein domain
:
Interleukin-10 receptor 1, IL-10R1
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d1y6kr1
R:2-100
2b
d1y6kr2
R:101-206
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1y6kL00 (L:12-156)
2a: CATH_1y6kR02 (R:104-206)
2b: CATH_1y6kR01 (R:2-103)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
1y6kL00
L:12-156
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1y6kR02
R:104-206
2b
1y6kR01
R:2-103
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_IL10_1y6kL01 (L:12-156)
2a: PFAM_Tissue_fac_1y6kR01 (R:2-90)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
4H_Cytokine
(48)
Family
:
IL10
(7)
Homo sapiens (Human)
(3)
1a
IL10-1y6kL01
L:12-156
Clan
:
E-set
(290)
Family
:
Tissue_fac
(23)
Homo sapiens (Human)
(23)
2a
Tissue_fac-1y6kR01
R:2-90
[
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 L
Chain R
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 (64 KB)
Header - Asym.Unit
Biol.Unit 1 (117 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
1Y6K
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help