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.
2ORV
Asym. Unit
Info
Asym.Unit (63 KB)
Biol.Unit 1 (110 KB)
Biol.Unit 2 (56 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN THYMIDINE KINASE 1 IN COMPLEX WITH TP4A
Authors
:
D. Segura-Pena, S. Lutz, C. Monnerjahn, M. Konrad, A. Lavie
Date
:
04 Feb 07 (Deposition) - 27 Mar 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Biol. Unit 2: A,B (1x)
Keywords
:
Tk-1 (Thymidine Kinase 1), Tp4A (P1-(5'-Adenosyl)P4-(5'- (2'Deoxythymidil))Tetraphosphate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Segura-Pena, S. Lutz, C. Monnerjahn, M. Konrad, A. Lavie
Binding Of Atp To Tk1-Like Enzymes Is Associated With A Conformational Change In The Quaternary Structure.
J. Mol. Biol. V. 369 129 2007
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-T... (4TAa)
1b: P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-T... (4TAb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4TA
2
Ligand/Ion
P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
2
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:153 , CYS A:156 , CYS A:185 , CYS A:188
BINDING SITE FOR RESIDUE ZN A 235
2
AC2
SOFTWARE
CYS B:153 , CYS B:156 , CYS B:185 , CYS B:188
BINDING SITE FOR RESIDUE ZN B 235
3
AC3
SOFTWARE
MET A:28 , PHE A:29 , SER A:30 , GLY A:31 , LYS A:32 , SER A:33 , ASP A:58 , ARG A:60 , ASP A:97 , GLU A:98 , GLN A:100 , PHE A:101 , LEU A:124 , THR A:127 , PHE A:128 , PHE A:133 , VAL A:172 , GLU A:173 , VAL A:174 , ILE A:175 , GLY A:176 , TYR A:181 , HOH A:806 , HOH A:810 , HOH A:823 , HOH A:831 , HOH A:846 , HOH A:863 , HOH A:868 , HOH A:880
BINDING SITE FOR RESIDUE 4TA A 801
4
AC4
SOFTWARE
MET B:28 , PHE B:29 , SER B:30 , GLY B:31 , LYS B:32 , SER B:33 , ASP B:58 , ASP B:97 , GLU B:98 , GLN B:100 , PHE B:101 , LEU B:124 , THR B:127 , PHE B:128 , PHE B:133 , THR B:163 , ARG B:165 , VAL B:172 , GLU B:173 , VAL B:174 , ILE B:175 , GLY B:176 , TYR B:181 , HOH B:808 , HOH B:821 , HOH B:834 , HOH B:872
BINDING SITE FOR RESIDUE 4TA B 802
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: TK_CELLULAR_TYPE (A:176-189,B:176-189)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TK_CELLULAR_TYPE
PS00603
Thymidine kinase cellular-type signature.
KITH_HUMAN
176-189
2
A:176-189
B:176-189
[
close PROSITE info
]
Exons
(7, 14)
Info
All Exons
Exon 1.1a (A:18-22 | B:18-22)
Exon 1.2 (A:23-33 | B:23-33)
Exon 1.3 (A:33-61 | B:33-58)
Exon 1.4 (A:73-101 | B:73-101)
Exon 1.5 (A:102-131 | B:102-131)
Exon 1.6 (A:132-171 | B:132-171)
Exon 1.7b (A:172-191 | B:172-191)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7b
8: 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
1.1a
ENST00000301634
1a
ENSE00001563417
chr17:
76183314-76183010
305
KITH_HUMAN
1-22
22
2
A:18-22
B:18-22
5
5
1.2
ENST00000301634
2
ENSE00001118176
chr17:
76182899-76182868
32
KITH_HUMAN
23-33
11
2
A:23-33
B:23-33
11
11
1.3
ENST00000301634
3
ENSE00001194741
chr17:
76181246-76181136
111
KITH_HUMAN
33-70
38
2
A:33-61
B:33-58
29
26
1.4
ENST00000301634
4
ENSE00001118177
chr17:
76178763-76178670
94
KITH_HUMAN
70-101
32
2
A:73-101
B:73-101
29
29
1.5
ENST00000301634
5
ENSE00001118174
chr17:
76171699-76171610
90
KITH_HUMAN
102-131
30
2
A:102-131
B:102-131
30
30
1.6
ENST00000301634
6
ENSE00001118182
chr17:
76171250-76171131
120
KITH_HUMAN
132-171
40
2
A:132-171
B:132-171
40
40
1.7b
ENST00000301634
7b
ENSE00001274786
chr17:
76171031-76170160
872
KITH_HUMAN
172-234
63
2
A:172-191
B:172-191
20
20
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2orva1 (A:18-150)
1b: SCOP_d2orvb1 (B:18-150)
2a: SCOP_d2orva2 (A:151-191)
2b: SCOP_d2orvb2 (B:151-191)
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
:
Type II thymidine kinase
(8)
Protein domain
:
Thymidine kinase, TK1, N-terminal domain
(6)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2orva1
A:18-150
1b
d2orvb1
B:18-150
Class
:
Small proteins
(3458)
Fold
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Superfamily
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Family
:
Type II thymidine kinase zinc finger
(6)
Protein domain
:
Thymidine kinase, TK1, C-terminal domain
(6)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2orva2
A:151-191
2b
d2orvb2
B:151-191
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (63 KB)
Header - Asym.Unit
Biol.Unit 1 (110 KB)
Header - Biol.Unit 1
Biol.Unit 2 (56 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
2ORV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
