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.
2UYY
Asym. Unit
Info
Asym.Unit (194 KB)
Biol.Unit 1 (185 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE CYTOKINE-LIKE NUCLEAR FACTOR N-PAC
Authors
:
J. Tickle, E. S. Pilka, G. Bunkoczi, G. Berridge, C. Smee, K. L. Kavanagh V. Hozjan, F. H. Niesen, E. Papagrigoriou, A. C. W. Pike, A. Turnbull, C. H. Arrowsmith, A. Edwards, M. Sundstrom, J. Weigelt, F. Von Delft, U. Oppermann
Date
:
20 Apr 07 (Deposition) - 03 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Long-Chain Dehydrogenase, Cytokine
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Tickle, E. S. Pilka, G. Bunkoczi, G. Berridge, C. Smee, K. L. Kavanagh, V. Hozjan, F. H. Niesen, E. Papagrigoriou, A. C. W. Pike A. Turnbull, C. H. Arrowsmith, A. Edwards, M. Sundstrom, J. Weigelt, F. Von Delft, U. Oppermann
The Structure Of The Cytokine-Like Nuclear Factor N-Pac
To Be Published
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN... (NA7a)
2b: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN... (NA7b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
4
Ligand/Ion
POTASSIUM ION
2
NA7
2
Ligand/Ion
[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:397 , GLN A:418 , ALA A:419 , GLY A:421 , HOH A:2039
BINDING SITE FOR RESIDUE K A1554
2
AC2
SOFTWARE
GLY B:397 , GLN B:418 , ALA B:419 , GLY B:421 , HOH B:2033
BINDING SITE FOR RESIDUE K B1554
3
AC3
SOFTWARE
GLY C:397 , GLN C:418 , ALA C:419 , GLY C:421 , HOH C:2035 , HOH C:2045
BINDING SITE FOR RESIDUE K C1554
4
AC4
SOFTWARE
GLY D:397 , GLN D:418 , ALA D:419 , GLY D:421 , HOH D:2044
BINDING SITE FOR RESIDUE K D1554
5
AC5
SOFTWARE
GLY A:276 , LEU A:277 , MET A:278 , ASN A:297 , ARG A:298 , THR A:299 , LYS A:302 , CYS A:330 , VAL A:331 , SER A:332 , ALA A:336 , ASP A:339 , THR A:362 , TYR A:499 , TYR A:502 , LYS A:505 , HOH A:2089 , HOH A:2090 , HOH A:2091
BINDING SITE FOR RESIDUE NA7 A1555
6
AC6
SOFTWARE
LEU D:275 , GLY D:276 , LEU D:277 , MET D:278 , ASN D:297 , ARG D:298 , THR D:299 , CYS D:330 , VAL D:331 , SER D:332 , ALA D:336 , ASP D:339 , THR D:362 , PHE D:498 , TYR D:499 , TYR D:502 , LYS D:505 , HOH D:2100 , HOH D:2101 , HOH D:2102
BINDING SITE FOR RESIDUE NA7 D1555
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_037404 (Q459Q, chain A/B/C/D, )
2: VAR_037405 (Y531C, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_037404
H
459
Q
GLYR1_HUMAN
Polymorphism
2085329
A/B/C/D
Q
459
Q
2
UniProt
VAR_037405
Y
531
C
GLYR1_HUMAN
Polymorphism
17703111
A/B/C/D
Y
531
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.9 (A:262-269 | B:262-269 | C:262-269 ...)
Exon 1.10 (A:269-302 | B:269-302 | C:269-302 ...)
Exon 1.11a (A:303-339 | B:303-339 | C:303-339 ...)
Exon 1.12 (A:340-373 | B:340-373 | C:340-373 ...)
Exon 1.13 (A:374-428 | B:374-428 | C:374-428 ...)
Exon 1.14 (A:428-488 | B:428-488 | C:428-488 ...)
Exon 1.15 (A:488-529 | B:488-529 | C:488-529 ...)
Exon 1.16b (A:530-553 | B:530-553 | C:530-553 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.8/1.9
2: Boundary 1.9/1.10
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 1.14/1.15
8: Boundary 1.15/1.16b
9: Boundary 1.16b/-
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
ENST00000321919
1a
ENSE00000944218
chr16:
4897343-4897229
115
GLYR1_HUMAN
1-13
13
0
-
-
1.2
ENST00000321919
2
ENSE00001145253
chr16:
4896211-4896175
37
GLYR1_HUMAN
13-25
13
0
-
-
1.3
ENST00000321919
3
ENSE00000944205
chr16:
4895154-4895075
80
GLYR1_HUMAN
26-52
27
0
-
-
1.4
ENST00000321919
4
ENSE00000944206
chr16:
4882913-4882775
139
GLYR1_HUMAN
52-98
47
0
-
-
1.5
ENST00000321919
5
ENSE00000944207
chr16:
4882222-4881980
243
GLYR1_HUMAN
99-179
81
0
-
-
1.6
ENST00000321919
6
ENSE00000944208
chr16:
4873908-4873822
87
GLYR1_HUMAN
180-208
29
0
-
-
1.7
ENST00000321919
7
ENSE00000944209
chr16:
4872932-4872876
57
GLYR1_HUMAN
209-227
19
0
-
-
1.8
ENST00000321919
8
ENSE00000944220
chr16:
4871598-4871548
51
GLYR1_HUMAN
228-244
17
0
-
-
1.9
ENST00000321919
9
ENSE00000944210
chr16:
4871454-4871381
74
GLYR1_HUMAN
245-269
25
4
A:262-269
B:262-269
C:262-269
D:263-269
8
8
8
7
1.10
ENST00000321919
10
ENSE00000944211
chr16:
4867698-4867599
100
GLYR1_HUMAN
269-302
34
4
A:269-302
B:269-302
C:269-302
D:269-302
34
34
34
34
1.11a
ENST00000321919
11a
ENSE00001192716
chr16:
4864648-4864538
111
GLYR1_HUMAN
303-339
37
4
A:303-339
B:303-339
C:303-339
D:303-339
37
37
37
37
1.12
ENST00000321919
12
ENSE00000944213
chr16:
4863839-4863738
102
GLYR1_HUMAN
340-373
34
4
A:340-373
B:340-373
C:340-373
D:340-373
34
34
34
34
1.13
ENST00000321919
13
ENSE00000944214
chr16:
4862249-4862087
163
GLYR1_HUMAN
374-428
55
4
A:374-428
B:374-428
C:374-428
D:374-428
55
55
55
55
1.14
ENST00000321919
14
ENSE00000944215
chr16:
4861803-4861624
180
GLYR1_HUMAN
428-488
61
4
A:428-488
B:428-488
C:428-488
D:428-488
61
61
61
61
1.15
ENST00000321919
15
ENSE00000944216
chr16:
4861295-4861171
125
GLYR1_HUMAN
488-529
42
4
A:488-529
B:488-529
C:488-529
D:488-529
42
42
42
42
1.16b
ENST00000321919
16b
ENSE00000944217
chr16:
4855311-4853204
2108
GLYR1_HUMAN
530-553
24
4
A:530-553
B:530-553
C:530-553
D:530-553
24
24
24
24
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2uyya2 (A:430-553)
1b: SCOP_d2uyyb2 (B:430-553)
1c: SCOP_d2uyyc2 (C:430-553)
1d: SCOP_d2uyyd2 (D:430-553)
2a: SCOP_d2uyya1 (A:262-429)
2b: SCOP_d2uyyb1 (B:262-429)
2c: SCOP_d2uyyc1 (C:262-429)
2d: SCOP_d2uyyd1 (D:263-429)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d2uyya2
A:430-553
1b
d2uyyb2
B:430-553
1c
d2uyyc2
C:430-553
1d
d2uyyd2
D:430-553
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Human (Homo sapiens) [TaxId: 9606]
(32)
2a
d2uyya1
A:262-429
2b
d2uyyb1
B:262-429
2c
d2uyyc1
C:262-429
2d
d2uyyd1
D:263-429
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_NAD_binding_2_2uyyD01 (D:267-429)
1b: PFAM_NAD_binding_2_2uyyD02 (D:267-429)
1c: PFAM_NAD_binding_2_2uyyD03 (D:267-429)
1d: PFAM_NAD_binding_2_2uyyD04 (D:267-429)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_binding_2
(15)
Homo sapiens (Human)
(2)
1a
NAD_binding_2-2uyyD01
D:267-429
1b
NAD_binding_2-2uyyD02
D:267-429
1c
NAD_binding_2-2uyyD03
D:267-429
1d
NAD_binding_2-2uyyD04
D:267-429
[
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
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 (194 KB)
Header - Asym.Unit
Biol.Unit 1 (185 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
2UYY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
