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.
3EHW
Asym. Unit
Info
Asym.Unit (156 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (78 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN DUTPASE IN COMPLEX WITH ALPHA,BETA-IMIDO-DUTP AND MG2+: VISUALIZATION OF THE FULL-LENGTH C-TERMINI IN ALL MONOMERS AND SUGGESTION FOR AN ADDITIONAL METAL ION BINDING SITE
Authors
:
E. Takacs, O. Barabas, B. G. Vertessy
Date
:
15 Sep 08 (Deposition) - 30 Sep 08 (Release) - 07 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,X,Y,Z
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: X,Y,Z (1x)
Keywords
:
Jelly-Roll, Full-Length C-Terminal Arm, Enzyme-Ligand Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Takacs, O. Barabas, B. G. Vertessy
Human Dutpase In Complex With Alpha, Beta-Imido-Dutp And Mg2+: Visualization Of The Full-Length C-Termini In All Monomers And Suggestion For An Additional Metal Ion Binding Site
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 14)
Info
All Hetero Components
1a: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPa)
1b: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPb)
1c: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPc)
1d: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPd)
1e: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPe)
1f: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMID... (DUPf)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DUP
6
Ligand/Ion
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:85 , SER A:86 , GLY A:87 , GLN A:131 , MG A:165 , HOH A:850 , HOH A:854 , ALA B:98 , GLY B:99 , VAL B:100 , ILE B:101 , ASP B:102 , TYR B:105 , GLY B:110 , HOH B:778 , ARG C:153 , GLY C:157 , PHE C:158 , GLY C:159 , SER C:160 , THR C:161 , HOH C:780 , HOH C:857 , HOH X:790 , HOH X:856
BINDING SITE FOR RESIDUE DUP C 777
02
AC2
SOFTWARE
HOH A:850 , HOH A:854 , DUP C:777 , HOH C:857
BINDING SITE FOR RESIDUE MG A 165
03
AC3
SOFTWARE
DUP B:777 , HOH B:849 , HOH C:855 , HOH X:874
BINDING SITE FOR RESIDUE MG C 778
04
AC4
SOFTWARE
DUP A:777 , HOH B:796 , HOH B:856 , HOH X:888
BINDING SITE FOR RESIDUE MG B 165
05
AC5
SOFTWARE
DUP Y:777 , HOH Y:854 , HOH Z:779 , HOH Z:836
BINDING SITE FOR RESIDUE MG Z 165
06
AC6
SOFTWARE
HOH X:828 , HOH X:990 , DUP Z:777 , HOH Z:839
BINDING SITE FOR RESIDUE MG X 165
07
AC7
SOFTWARE
DUP X:777 , HOH X:920 , HOH X:993 , HOH Y:852
BINDING SITE FOR RESIDUE MG Y 165
08
AC8
SOFTWARE
ALA A:98 , GLY A:99 , VAL A:100 , ILE A:101 , ASP A:102 , TYR A:105 , GLY A:110 , HOH A:779 , ARG B:153 , GLY B:157 , PHE B:158 , GLY B:159 , SER B:160 , THR B:161 , HOH B:779 , HOH B:780 , HOH B:849 , ARG C:85 , SER C:86 , GLY C:87 , GLN C:131 , MG C:778 , HOH C:855 , HOH X:784 , HOH X:874
BINDING SITE FOR RESIDUE DUP B 777
09
AC9
SOFTWARE
ARG A:153 , GLY A:157 , PHE A:158 , GLY A:159 , SER A:160 , THR A:161 , HOH A:783 , ARG B:85 , SER B:86 , GLY B:87 , GLN B:131 , MG B:165 , HOH B:796 , HOH B:856 , ALA C:98 , GLY C:99 , VAL C:100 , ILE C:101 , ASP C:102 , TYR C:105 , GLY C:110 , HOH X:786 , HOH X:799 , HOH X:800 , HOH X:888
BINDING SITE FOR RESIDUE DUP A 777
10
BC1
SOFTWARE
ALA X:98 , GLY X:99 , VAL X:100 , ILE X:101 , ASP X:102 , TYR X:105 , ASN X:108 , GLY X:110 , HOH X:796 , HOH X:849 , HOH X:868 , ARG Y:153 , GLY Y:157 , PHE Y:158 , GLY Y:159 , SER Y:160 , THR Y:161 , HOH Y:780 , HOH Y:854 , ARG Z:85 , SER Z:86 , GLY Z:87 , GLN Z:131 , MG Z:165 , HOH Z:779 , HOH Z:836
BINDING SITE FOR RESIDUE DUP Y 777
11
BC2
SOFTWARE
ARG X:85 , SER X:86 , GLY X:87 , GLN X:131 , MG X:165 , HOH X:788 , HOH X:828 , HOH X:990 , ALA Y:98 , GLY Y:99 , VAL Y:100 , ILE Y:101 , ASP Y:102 , TYR Y:105 , GLY Y:110 , HOH Y:778 , ARG Z:153 , GLY Z:157 , PHE Z:158 , GLY Z:159 , SER Z:160 , THR Z:161 , HOH Z:781 , HOH Z:782 , HOH Z:839
BINDING SITE FOR RESIDUE DUP Z 777
12
BC3
SOFTWARE
ARG X:153 , GLY X:157 , PHE X:158 , GLY X:159 , SER X:160 , THR X:161 , HOH X:779 , HOH X:783 , HOH X:831 , HOH X:920 , HOH X:993 , ARG Y:85 , SER Y:86 , GLY Y:87 , GLN Y:131 , MG Y:165 , HOH Y:852 , ALA Z:98 , GLY Z:99 , VAL Z:100 , ILE Z:101 , ASP Z:102 , TYR Z:105 , GLY Z:110 , HOH Z:778
BINDING SITE FOR RESIDUE DUP X 777
13
BC4
SOFTWARE
ASP X:95 , HOH X:953 , HOH X:960 , HOH X:994 , ASP Y:95 , HOH Y:824 , ASP Z:95
BINDING SITE FOR RESIDUE MG X 778
14
BC5
SOFTWARE
ASP A:95 , HOH A:839 , HOH A:852 , ASP B:95 , HOH B:803 , HOH B:883 , ASP C:95
BINDING SITE FOR RESIDUE MG A 778
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(6, 36)
Info
All Exons
Exon 1.2b (A:24-52 | B:25-52 | C:25-52 | X:25...)
Exon 1.3 (A:52-83 | B:52-83 | C:52-83 | X:52...)
Exon 1.4 (A:83-98 | B:83-98 | C:83-98 | X:83...)
Exon 1.5 (A:98-123 | B:98-123 | C:98-123 | X...)
Exon 1.6 (A:123-146 | B:123-146 | C:123-146 ...)
Exon 1.7b (A:147-164 | B:147-164 | C:147-164 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1b/1.2b
2: Boundary 1.2b/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7b
7: Boundary 1.7b/-
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
1.1b
ENST00000331200
1b
ENSE00001487133
chr15:
48623621-48623992
372
DUT_HUMAN
1-94
94
0
-
-
1.2b
ENST00000331200
2b
ENSE00001789447
chr15:
48624465-48624603
139
DUT_HUMAN
94-140
47
6
A:24-52
B:25-52
C:25-52
X:25-52
Y:25-52
Z:25-52
29
28
28
28
28
28
1.3
ENST00000331200
3
ENSE00000686853
chr15:
48626614-48626705
92
DUT_HUMAN
140-171
32
6
A:52-83
B:52-83
C:52-83
X:52-83
Y:52-83
Z:52-83
32
32
32
32
32
32
1.4
ENST00000331200
4
ENSE00000686856
chr15:
48628243-48628287
45
DUT_HUMAN
171-186
16
6
A:83-98
B:83-98
C:83-98
X:83-98
Y:83-98
Z:83-98
16
16
16
16
16
16
1.5
ENST00000331200
5
ENSE00000686860
chr15:
48633486-48633560
75
DUT_HUMAN
186-211
26
6
A:98-123
B:98-123
C:98-123
X:98-123
Y:98-123
Z:98-123
26
26
26
26
26
26
1.6
ENST00000331200
6
ENSE00000884477
chr15:
48633712-48633782
71
DUT_HUMAN
211-234
24
6
A:123-146
B:123-146
C:123-146
X:123-146
Y:123-146
Z:123-146
24
24
24
24
24
24
1.7b
ENST00000331200
7b
ENSE00001030201
chr15:
48634219-48635570
1352
DUT_HUMAN
235-252
18
6
A:147-164
B:147-164
C:147-164
X:147-164
Y:147-164
Z:147-164
18
18
18
18
18
18
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3ehwa_ (A:)
1b: SCOP_d3ehwy_ (Y:)
1c: SCOP_d3ehwz_ (Z:)
1d: SCOP_d3ehwb_ (B:)
1e: SCOP_d3ehwc_ (C:)
1f: SCOP_d3ehwx_ (X:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
dUTPase-like
(122)
Family
:
automated matches
(51)
Protein domain
:
automated matches
(51)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d3ehwa_
A:
1b
d3ehwy_
Y:
1c
d3ehwz_
Z:
1d
d3ehwb_
B:
1e
d3ehwc_
C:
1f
d3ehwx_
X:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3ehwA00 (A:24-164)
1b: CATH_3ehwB00 (B:25-164)
1c: CATH_3ehwC00 (C:25-164)
1d: CATH_3ehwX00 (X:25-164)
1e: CATH_3ehwY00 (Y:25-164)
1f: CATH_3ehwZ00 (Z:25-164)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
(52)
Homologous Superfamily
:
[code=2.70.40.10, no name defined]
(51)
Human (Homo sapiens)
(4)
1a
3ehwA00
A:24-164
1b
3ehwB00
B:25-164
1c
3ehwC00
C:25-164
1d
3ehwX00
X:25-164
1e
3ehwY00
Y:25-164
1f
3ehwZ00
Z:25-164
[
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 X
Chain Y
Chain Z
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 (156 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (78 KB)
Header - Biol.Unit 2
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
3EHW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
