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.
1YKB
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (147 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 INSECT CELL EXPRESSED IL-22
Authors
:
T. Xu, N. J. Logsdon, M. R. Walter
Date
:
17 Jan 05 (Deposition) - 12 Jul 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Interleukin, Cytokine, Il-22, Glycosylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Xu, N. J. Logsdon, M. R. Walter
Structure Of Insect-Cell-Derived Il-22.
Acta Crystallogr. , Sect. D V. 61 942 2005
[
close entry info
]
Hetero Components
(3, 19)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
1b: ALPHA-L-FUCOSE (FUCb)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
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)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
2
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:54 , MET A:58 , FUC A:1112 , NAG A:1113 , PHE B:47 , GLN B:48 , THR B:53 , PHE B:171 , ARG B:175
BINDING SITE FOR RESIDUE NAG A 1111
02
AC2
SOFTWARE
TYR A:51 , ARG A:55 , NAG A:1111 , NAG A:1113
BINDING SITE FOR RESIDUE FUC A 1112
03
AC3
SOFTWARE
NAG A:1111 , FUC A:1112 , GLN B:48
BINDING SITE FOR RESIDUE NAG A 1113
04
AC4
SOFTWARE
ASN A:97 , SER A:126 , HIS F:39 , ARG F:41
BINDING SITE FOR RESIDUE NAG A 1131
05
AC5
SOFTWARE
ASN B:97 , GLU B:101 , SER B:126
BINDING SITE FOR RESIDUE NAG B 1231
06
AC6
SOFTWARE
ASN C:97 , GLU C:101 , SER C:126 , NAG C:1332
BINDING SITE FOR RESIDUE NAG C 1331
07
AC7
SOFTWARE
NAG C:1331
BINDING SITE FOR RESIDUE NAG C 1332
08
AC8
SOFTWARE
PHE C:47 , PRO C:50 , THR C:53 , PHE C:171 , ARG C:175 , ASN D:54 , MET D:58 , NAG D:1412 , FUC D:1415
BINDING SITE FOR RESIDUE NAG D 1411
09
AC9
SOFTWARE
GLN C:48 , PRO C:50 , NAG D:1411 , MAN D:1413 , MAN D:1414
BINDING SITE FOR RESIDUE NAG D 1412
10
BC1
SOFTWARE
NAG D:1412 , MAN D:1414
BINDING SITE FOR RESIDUE MAN D 1413
11
BC2
SOFTWARE
NAG D:1412 , MAN D:1413 , ARG E:143
BINDING SITE FOR RESIDUE MAN D 1414
12
BC3
SOFTWARE
TYR D:51 , ARG D:55 , NAG D:1411
BINDING SITE FOR RESIDUE FUC D 1415
13
BC4
SOFTWARE
ASN D:97 , GLU D:101 , SER D:126 , NAG D:1432
BINDING SITE FOR RESIDUE NAG D 1431
14
BC5
SOFTWARE
NAG D:1431
BINDING SITE FOR RESIDUE NAG D 1432
15
BC6
SOFTWARE
ASN E:97 , GLU E:101 , SER E:126
BINDING SITE FOR RESIDUE NAG E 1531
16
BC7
SOFTWARE
PHE E:47 , THR E:53 , MET E:172 , ASN F:54 , ARG F:55 , MET F:58 , NAG F:1612
BINDING SITE FOR RESIDUE NAG F 1611
17
BC8
SOFTWARE
GLN E:48 , NAG F:1611
BINDING SITE FOR RESIDUE NAG F 1612
18
BC9
SOFTWARE
ASN F:97 , GLU F:101 , SER F:126 , NAG F:1632
BINDING SITE FOR RESIDUE NAG F 1631
19
CC1
SOFTWARE
NAG F:1631
BINDING SITE FOR RESIDUE NAG F 1632
[
close Site info
]
SAPs(SNPs)/Variants
(1, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_013078 (S158G, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_013078
S
158
G
IL22_HUMAN
Polymorphism
2227507
A/B/C/D/E/F
S
158
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: INTERLEUKIN_10 (A:84-104,B:84-104,C:84-104,D:84-10...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTERLEUKIN_10
PS00520
Interleukin-10 family signature.
IL22_HUMAN
84-104
6
A:84-104
B:84-104
C:84-104
D:84-104
E:84-104
F:84-104
[
close PROSITE info
]
Exons
(5, 30)
Info
All Exons
Exon 1.1 (A:39-62 | B:38-62 | C:38-62 | D:38...)
Exon 1.2 (A:63-84 | B:63-84 | C:63-84 | D:63...)
Exon 1.3 (A:85-132 | B:85-132 | C:85-132 | D...)
Exon 1.4 (A:133-154 | B:133-154 | C:133-154 ...)
Exon 1.5 (A:155-179 | B:155-179 | C:155-179 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/-
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
ENST00000328087
1
ENSE00001303127
chr12:
68647284-68647043
242
IL22_HUMAN
1-62
62
6
A:39-62
B:38-62
C:38-62
D:38-62
E:38-62
F:38-62
24
25
25
25
25
25
1.2
ENST00000328087
2
ENSE00000920698
chr12:
68646609-68646544
66
IL22_HUMAN
63-84
22
6
A:63-84
B:63-84
C:63-84
D:63-84
E:63-84
F:63-84
22
22
22
22
22
22
1.3
ENST00000328087
3
ENSE00000920697
chr12:
68646427-68646284
144
IL22_HUMAN
85-132
48
6
A:85-132
B:85-132
C:85-132
D:85-132
E:85-132
F:85-132
48
48
48
48
48
48
1.4
ENST00000328087
4
ENSE00001100627
chr12:
68645358-68645293
66
IL22_HUMAN
133-154
22
6
A:133-154
B:133-154
C:133-154
D:133-154
E:133-154
F:133-154
22
22
22
22
22
22
1.5
ENST00000328087
5
ENSE00001311233
chr12:
68642656-68642025
632
IL22_HUMAN
155-179
25
6
A:155-179
B:155-179
C:155-179
D:155-179
E:155-179
F:155-179
25
25
25
25
25
25
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1ykba_ (A:)
1b: SCOP_d1ykbb_ (B:)
1c: SCOP_d1ykbc_ (C:)
1d: SCOP_d1ykbd_ (D:)
1e: SCOP_d1ykbe_ (E:)
1f: SCOP_d1ykbf_ (F:)
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-22 (IL-22)
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1ykba_
A:
1b
d1ykbb_
B:
1c
d1ykbc_
C:
1d
d1ykbd_
D:
1e
d1ykbe_
E:
1f
d1ykbf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1ykbA00 (A:39-179)
1b: CATH_1ykbB00 (B:38-179)
1c: CATH_1ykbC00 (C:38-179)
1d: CATH_1ykbD00 (D:38-179)
1e: CATH_1ykbE00 (E:38-179)
1f: CATH_1ykbF00 (F:38-179)
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
1ykbA00
A:39-179
1b
1ykbB00
B:38-179
1c
1ykbC00
C:38-179
1d
1ykbD00
D:38-179
1e
1ykbE00
E:38-179
1f
1ykbF00
F:38-179
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain B
Chain C
Chain D
Chain E
Chain F
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 (153 KB)
Header - Asym.Unit
Biol.Unit 1 (147 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
1YKB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help