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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2PL3
Asym. Unit
Info
Asym.Unit (46 KB)
Biol.Unit 1 (40 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN DEAD-BOX RNA HELICASE DDX10, DEAD DOMAIN IN COMPLEX WITH ADP
Authors
:
T. Karlberg, L. Lehtio, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Co L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, B. M. Hal M. Hammarstrom, I. Johansson, A. Kallas, T. Kotenyova, M. Moche, P. No T. Nyman, C. Persson, J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Tho S. Van Den Berg, J. Weigelt, L. Holmberg-Schiavone, Structural Ge Consortium (Sgc)
Date
:
19 Apr 07 (Deposition) - 01 May 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Rna, Helicase, Dead, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Schutz, T. Karlberg, S. Van Den Berg, R. Collins, L. Lehtio, M. Hogbom, L. Holmberg-Schiavone, W. Tempel, H. W. Park, M. Hammarstrom, M. Moche, A. G. Thorsell, H. Schuler
Comparative Structural Analysis Of Human Dead-Box Rna Helicases.
Plos One V. 5 12791 2010
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: ETHANOL (EOHa)
2b: ETHANOL (EOHb)
2c: ETHANOL (EOHc)
2d: ETHANOL (EOHd)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
EOH
4
Ligand/Ion
ETHANOL
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
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
GLU A:223 , ADP A:300 , HOH A:404 , HOH A:405 , HOH A:406 , HOH A:469
BINDING SITE FOR RESIDUE MG A 301
2
AC2
SOFTWARE
SER A:45 , MET A:46 , GLN A:47 , ARG A:50 , PHE A:71 , TYR A:89 , LEU A:91 , GLN A:96 , THR A:115 , GLY A:116 , SER A:117 , GLY A:118 , LYS A:119 , THR A:120 , GLU A:223 , MG A:301 , HOH A:404 , HOH A:406 , HOH A:410 , HOH A:415 , HOH A:448 , HOH A:469
BINDING SITE FOR RESIDUE ADP A 300
3
AC3
SOFTWARE
LEU A:153
BINDING SITE FOR RESIDUE EOH A 400
4
AC4
SOFTWARE
GLN A:98 , GLN A:256 , LYS A:258 , LYS A:261 , HOH A:417
BINDING SITE FOR RESIDUE EOH A 401
5
AC5
SOFTWARE
ALA A:112 , ALA A:254 , TRP A:275 , VAL A:276 , HIS A:277
BINDING SITE FOR RESIDUE EOH A 402
6
AC6
SOFTWARE
ALA A:233 , ASN A:237 , LEU A:263 , LEU A:266
BINDING SITE FOR RESIDUE EOH A 403
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: Q_MOTIF (A:69-97)
2: DEAD_ATP_HELICASE (A:220-228)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
Q_MOTIF
PS51195
DEAD-box RNA helicase Q motif profile.
DDX10_HUMAN
69-97
1
A:69-97
2
DEAD_ATP_HELICASE
PS00039
DEAD-box subfamily ATP-dependent helicases signature.
DDX10_HUMAN
220-228
1
A:220-228
[
close PROSITE info
]
Exons
(6, 6)
Info
All Exons
Exon 1.1a (A:45-62)
Exon 1.2 (A:63-83)
Exon 1.3a (A:83-126)
Exon 1.4 (A:127-178)
Exon 1.5 (A:181-220)
Exon 1.6a (A:220-278)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2
3: Boundary 1.2/1.3a
4: Boundary 1.3a/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6a
7: Boundary 1.6a/1.7
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
ENST00000322536
1a
ENSE00002146160
chr11:
108535752-108536066
315
DDX10_HUMAN
1-62
62
1
A:45-62
18
1.2
ENST00000322536
2
ENSE00001005166
chr11:
108544194-108544254
61
DDX10_HUMAN
63-83
21
1
A:63-83
21
1.3a
ENST00000322536
3a
ENSE00001005161
chr11:
108546323-108546453
131
DDX10_HUMAN
83-126
44
1
A:83-126
44
1.4
ENST00000322536
4
ENSE00001224552
chr11:
108547812-108547970
159
DDX10_HUMAN
127-179
53
1
A:127-178
52
1.5
ENST00000322536
5
ENSE00001309598
chr11:
108549042-108549162
121
DDX10_HUMAN
180-220
41
1
A:181-220
40
1.6a
ENST00000322536
6a
ENSE00001291421
chr11:
108550098-108550287
190
DDX10_HUMAN
220-283
64
1
A:220-278
59
1.7
ENST00000322536
7
ENSE00001307885
chr11:
108559663-108559789
127
DDX10_HUMAN
283-325
43
0
-
-
1.8
ENST00000322536
8
ENSE00001317728
chr11:
108562603-108562765
163
DDX10_HUMAN
326-380
55
0
-
-
1.9
ENST00000322536
9
ENSE00001005159
chr11:
108564243-108564327
85
DDX10_HUMAN
380-408
29
0
-
-
1.10
ENST00000322536
10
ENSE00001224211
chr11:
108577466-108577564
99
DDX10_HUMAN
408-441
34
0
-
-
1.11
ENST00000322536
11
ENSE00001295492
chr11:
108586606-108586693
88
DDX10_HUMAN
441-470
30
0
-
-
1.12
ENST00000322536
12
ENSE00001325848
chr11:
108590524-108590612
89
DDX10_HUMAN
471-500
30
0
-
-
1.13
ENST00000322536
13
ENSE00001224190
chr11:
108593724-108594189
466
DDX10_HUMAN
500-655
156
0
-
-
1.16b
ENST00000322536
16b
ENSE00001102046
chr11:
108709173-108709292
120
DDX10_HUMAN
656-695
40
0
-
-
1.17
ENST00000322536
17
ENSE00001102034
chr11:
108712042-108712203
162
DDX10_HUMAN
696-749
54
0
-
-
1.18
ENST00000322536
18
ENSE00001102064
chr11:
108722880-108722936
57
DDX10_HUMAN
750-768
19
0
-
-
1.21b
ENST00000322536
21b
ENSE00001224158
chr11:
108788600-108788745
146
DDX10_HUMAN
769-817
49
0
-
-
1.23d
ENST00000322536
23d
ENSE00002169559
chr11:
108810973-108811657
685
DDX10_HUMAN
817-875
59
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2pl3a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
automated matches
(303)
Protein domain
:
automated matches
(303)
Human (Homo sapiens) [TaxId: 9606]
(86)
1a
d2pl3a_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2pl3A00 (A:45-278)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
2pl3A00
A:45-278
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_DEAD_2pl3A01 (A:93-263)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
DEAD
(41)
Homo sapiens (Human)
(12)
1a
DEAD-2pl3A01
A:93-263
[
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 (46 KB)
Header - Asym.Unit
Biol.Unit 1 (40 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
2PL3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help