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2WVJ
Asym. Unit
Info
Asym.Unit (238 KB)
Biol.Unit 1 (116 KB)
Biol.Unit 2 (118 KB)
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(1)
Title
:
MUTATION OF THR163 TO SER IN HUMAN THYMIDINE KINASE SHIFTS THE SPECIFICITY FROM THYMIDINE TOWARDS THE NUCLEOSIDE ANALOGUE AZIDOTHYMIDINE
Authors
:
T. Skovgaard, U. Uhlin, B. Munch-Petersen
Date
:
17 Oct 09 (Deposition) - 27 Oct 09 (Release) - 02 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Zinc-Binding Domain, Deoxyribonucleoside Kinase, Feedback Inhibitor, Nucleotide-Binding, Kinase, Cytoplasm, Transferase, Atp-Binding, Dna Synthesis, Phosphoprotein, Phosphorylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Skovgaard, U. Uhlin, B. Munch-Petersen
Comparative Active-Site Mutation Study Of Human And Caenorhabditis Elegans Thymidine Kinase 1.
Febs J. V. 279 1777 2012
[
close entry info
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Hetero Components
(3, 19)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
2a: THYMIDINE-5'-TRIPHOSPHATE (TTPa)
2b: THYMIDINE-5'-TRIPHOSPHATE (TTPb)
2c: THYMIDINE-5'-TRIPHOSPHATE (TTPc)
2d: THYMIDINE-5'-TRIPHOSPHATE (TTPd)
2e: THYMIDINE-5'-TRIPHOSPHATE (TTPe)
2f: THYMIDINE-5'-TRIPHOSPHATE (TTPf)
2g: THYMIDINE-5'-TRIPHOSPHATE (TTPg)
2h: THYMIDINE-5'-TRIPHOSPHATE (TTPh)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
3
Ligand/Ion
MAGNESIUM ION
2
TTP
8
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
3
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
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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
MET A:28 , 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 , SER A:163 , VAL A:172 , GLU A:173 , VAL A:174 , ILE A:175 , GLY A:176 , TYR A:181 , HOH A:2116 , HOH A:2117 , HOH A:2118 , HOH A:2119
BINDING SITE FOR RESIDUE TTP A1192
02
AC2
SOFTWARE
SER B:30 , GLY B:31 , LYS B:32 , SER B:33 , ASP B:58 , ARG B:60 , ASP B:97 , GLU B:98 , GLN B:100 , PHE B:101 , LEU B:124 , THR B:127 , PHE B:128 , PHE B:133 , SER B:163 , VAL B:172 , GLU B:173 , VAL B:174 , ILE B:175 , GLY B:176 , TYR B:181 , HOH B:2135 , HOH B:2136 , HOH B:2137 , HOH B:2139
BINDING SITE FOR RESIDUE TTP B1193
03
AC3
SOFTWARE
MET C:28 , SER C:30 , GLY C:31 , LYS C:32 , SER C:33 , ASP C:58 , ARG C:60 , ASP C:97 , GLU C:98 , GLN C:100 , PHE C:101 , LEU C:124 , THR C:127 , PHE C:128 , PHE C:133 , SER C:163 , VAL C:172 , GLU C:173 , VAL C:174 , ILE C:175 , GLY C:176 , TYR C:181 , HOH C:2119 , HOH C:2120 , HOH C:2121 , HOH C:2123
BINDING SITE FOR RESIDUE TTP C1192
04
AC4
SOFTWARE
MET D:28 , PHE D:29 , SER D:30 , GLY D:31 , LYS D:32 , SER D:33 , ASP D:58 , ARG D:60 , GLU D:98 , PHE D:101 , LEU D:124 , THR D:127 , PHE D:128 , PHE D:133 , SER D:163 , ARG D:165 , VAL D:172 , GLU D:173 , VAL D:174 , ILE D:175 , GLY D:176 , TYR D:181 , MG D:1193 , HOH D:2056 , HOH D:2135 , HOH D:2136 , HOH D:2137 , HOH D:2138
BINDING SITE FOR RESIDUE TTP D1192
05
AC5
SOFTWARE
MET E:28 , SER E:30 , GLY E:31 , LYS E:32 , SER E:33 , ASP E:58 , ARG E:60 , ASP E:97 , GLU E:98 , GLN E:100 , PHE E:101 , LEU E:124 , THR E:127 , PHE E:128 , PHE E:133 , SER E:163 , ARG E:165 , VAL E:172 , GLU E:173 , VAL E:174 , ILE E:175 , GLY E:176 , TYR E:181 , HOH E:2116 , HOH E:2117 , HOH E:2119
BINDING SITE FOR RESIDUE TTP E1192
06
AC6
SOFTWARE
MET F:28 , SER F:30 , GLY F:31 , LYS F:32 , SER F:33 , ASP F:58 , ASP F:97 , GLU F:98 , GLN F:100 , PHE F:101 , LEU F:124 , THR F:127 , PHE F:128 , PHE F:133 , SER F:163 , VAL F:172 , GLU F:173 , VAL F:174 , ILE F:175 , GLY F:176 , TYR F:181 , HOH F:2116 , HOH F:2117 , HOH F:2118
BINDING SITE FOR RESIDUE TTP F1192
07
AC7
SOFTWARE
MET G:28 , PHE G:29 , SER G:30 , GLY G:31 , LYS G:32 , SER G:33 , ASP G:58 , ARG G:60 , GLU G:98 , PHE G:101 , LEU G:124 , THR G:127 , PHE G:128 , PHE G:133 , SER G:163 , ARG G:165 , VAL G:172 , GLU G:173 , VAL G:174 , ILE G:175 , GLY G:176 , TYR G:181 , MG G:1193 , HOH G:2061 , HOH G:2093 , HOH G:2162 , HOH G:2163 , HOH G:2164
BINDING SITE FOR RESIDUE TTP G1192
08
AC8
SOFTWARE
MET H:28 , PHE H:29 , SER H:30 , GLY H:31 , LYS H:32 , SER H:33 , ASP H:58 , ARG H:60 , GLU H:98 , PHE H:101 , LEU H:124 , THR H:127 , PHE H:128 , PHE H:133 , SER H:163 , ARG H:165 , VAL H:172 , GLU H:173 , VAL H:174 , ILE H:175 , GLY H:176 , TYR H:181 , MG H:1193 , HOH H:2150 , HOH H:2151 , HOH H:2152 , HOH H:2153
BINDING SITE FOR RESIDUE TTP H1192
09
AC9
SOFTWARE
SER D:33 , TTP D:1192 , HOH D:2009 , HOH D:2056 , HOH D:2057
BINDING SITE FOR RESIDUE MG D1193
10
BC1
SOFTWARE
SER G:33 , TTP G:1192 , HOH G:2014 , HOH G:2092
BINDING SITE FOR RESIDUE MG G1193
11
BC2
SOFTWARE
SER H:33 , TTP H:1192 , HOH H:2013 , HOH H:2077
BINDING SITE FOR RESIDUE MG H1193
12
BC3
SOFTWARE
CYS A:153 , CYS A:156 , CYS A:185 , CYS A:188
BINDING SITE FOR RESIDUE ZN A1193
13
BC4
SOFTWARE
CYS B:153 , CYS B:156 , CYS B:185 , CYS B:188
BINDING SITE FOR RESIDUE ZN B1194
14
BC5
SOFTWARE
CYS C:153 , CYS C:156 , CYS C:185 , CYS C:188
BINDING SITE FOR RESIDUE ZN C1193
15
BC6
SOFTWARE
CYS D:153 , CYS D:156 , CYS D:185 , CYS D:188
BINDING SITE FOR RESIDUE ZN D1194
16
BC7
SOFTWARE
CYS E:153 , CYS E:156 , CYS E:185 , CYS E:188
BINDING SITE FOR RESIDUE ZN E1193
17
BC8
SOFTWARE
CYS F:153 , CYS F:156 , CYS F:185 , CYS F:188
BINDING SITE FOR RESIDUE ZN F1193
18
BC9
SOFTWARE
CYS G:153 , CYS G:156 , CYS G:185 , CYS G:188
BINDING SITE FOR RESIDUE ZN G1194
19
CC1
SOFTWARE
CYS H:153 , CYS H:156 , CYS H:185 , CYS H:188
BINDING SITE FOR RESIDUE ZN H1194
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: TK_CELLULAR_TYPE (A:176-189,B:176-189,C:176-189,D:17...)
;
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
8
A:176-189
B:176-189
C:176-189
D:176-189
E:176-189
F:176-189
G:176-189
H:176-189
[
close PROSITE info
]
Exons
(7, 56)
Info
All Exons
Exon 1.1a (A:18-22 | B:18-22 | C:18-22 | D:18...)
Exon 1.2 (A:23-33 | B:23-33 | C:23-33 | D:23...)
Exon 1.3 (A:33-60 | B:33-60 | C:33-60 | D:33...)
Exon 1.4 (A:75-101 | B:75-101 | C:75-101 | D...)
Exon 1.5 (A:102-131 | B:102-131 | C:102-131 ...)
Exon 1.6 (A:132-171 | B:132-171 | C:132-171 ...)
Exon 1.7b (A:172-191 | B:172-192 | C: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
8
A:18-22
B:18-22
C:18-22
D:18-22
E:18-22
F:18-22
G:18-22
H:18-22
5
5
5
5
5
5
5
5
1.2
ENST00000301634
2
ENSE00001118176
chr17:
76182899-76182868
32
KITH_HUMAN
23-33
11
8
A:23-33
B:23-33
C:23-33
D:23-33
E:23-33
F:23-33
G:23-33
H:23-33
11
11
11
11
11
11
11
11
1.3
ENST00000301634
3
ENSE00001194741
chr17:
76181246-76181136
111
KITH_HUMAN
33-70
38
8
A:33-60
B:33-60
C:33-60
D:33-62
E:33-60
F:33-60
G:33-61
H:33-64
28
28
28
30
28
28
29
32
1.4
ENST00000301634
4
ENSE00001118177
chr17:
76178763-76178670
94
KITH_HUMAN
70-101
32
8
A:75-101
B:75-101
C:75-101
D:75-101
E:75-101
F:75-101
G:75-101
H:73-101
27
27
27
27
27
27
27
29
1.5
ENST00000301634
5
ENSE00001118174
chr17:
76171699-76171610
90
KITH_HUMAN
102-131
30
8
A:102-131
B:102-131
C:102-131
D:102-131
E:102-131
F:102-131
G:102-131
H:102-131
30
30
30
30
30
30
30
30
1.6
ENST00000301634
6
ENSE00001118182
chr17:
76171250-76171131
120
KITH_HUMAN
132-171
40
8
A:132-171
B:132-171
C:132-171
D:132-171
E:132-171
F:132-171
G:132-171
H:132-171
40
40
40
40
40
40
40
40
1.7b
ENST00000301634
7b
ENSE00001274786
chr17:
76171031-76170160
872
KITH_HUMAN
172-234
63
8
A:172-191
B:172-192
C:172-191
D:172-191
E:172-191
F:172-191
G:172-191
H:172-191
20
21
20
20
20
20
20
20
[
close EXON info
]
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d2wvja1 (A:18-150)
1b: SCOP_d2wvjc1 (C:18-150)
1c: SCOP_d2wvjd1 (D:18-150)
1d: SCOP_d2wvje1 (E:18-150)
1e: SCOP_d2wvjf1 (F:18-150)
1f: SCOP_d2wvjg1 (G:18-150)
1g: SCOP_d2wvjh1 (H:18-150)
1h: SCOP_d2wvjb1 (B:18-150)
2a: SCOP_d2wvja2 (A:151-191)
2b: SCOP_d2wvjc2 (C:151-191)
2c: SCOP_d2wvjd2 (D:151-191)
2d: SCOP_d2wvje2 (E:151-191)
2e: SCOP_d2wvjf2 (F:151-191)
2f: SCOP_d2wvjg2 (G:151-191)
2g: SCOP_d2wvjh2 (H:151-191)
2h: SCOP_d2wvjb2 (B:151-192)
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Protein Domains
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(
)
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
:
automated matches
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2wvja1
A:18-150
1b
d2wvjc1
C:18-150
1c
d2wvjd1
D:18-150
1d
d2wvje1
E:18-150
1e
d2wvjf1
F:18-150
1f
d2wvjg1
G:18-150
1g
d2wvjh1
H:18-150
1h
d2wvjb1
B:18-150
Class
:
Small proteins
(3458)
Fold
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Superfamily
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Family
:
automated matches
(14)
Protein domain
:
automated matches
(14)
Human (Homo sapiens) [TaxId: 9606]
(8)
2a
d2wvja2
A:151-191
2b
d2wvjc2
C:151-191
2c
d2wvjd2
D:151-191
2d
d2wvje2
E:151-191
2e
d2wvjf2
F:151-191
2f
d2wvjg2
G:151-191
2g
d2wvjh2
H:151-191
2h
d2wvjb2
B:151-192
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_TK_2wvjH01 (H:19-189)
1b: PFAM_TK_2wvjH02 (H:19-189)
1c: PFAM_TK_2wvjH03 (H:19-189)
1d: PFAM_TK_2wvjH04 (H:19-189)
1e: PFAM_TK_2wvjH05 (H:19-189)
1f: PFAM_TK_2wvjH06 (H:19-189)
1g: PFAM_TK_2wvjH07 (H:19-189)
1h: PFAM_TK_2wvjH08 (H:19-189)
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Clan
:
P-loop_NTPase
(1112)
Family
:
TK
(9)
Homo sapiens (Human)
(3)
1a
TK-2wvjH01
H:19-189
1b
TK-2wvjH02
H:19-189
1c
TK-2wvjH03
H:19-189
1d
TK-2wvjH04
H:19-189
1e
TK-2wvjH05
H:19-189
1f
TK-2wvjH06
H:19-189
1g
TK-2wvjH07
H:19-189
1h
TK-2wvjH08
H:19-189
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