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1XBT
Asym. Unit
Info
Asym.Unit (220 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (109 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN THYMIDINE KINASE 1
Authors
:
M. Welin, U. Kosinska, N. E. Mikkelsen, C. Carnrot, C. Zhu, L. Wang, S. Eriksson, B. Munch-Petersen, H. Eklund
Date
:
31 Aug 04 (Deposition) - 14 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
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
:
Deoxyribonucleoside Kinase, Zinc-Binding Domain, Feedback Inhibitor, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Welin, U. Kosinska, N. E. Mikkelsen, C. Carnrot, C. Zhu, L. Wang, S. Eriksson, B. Munch-Petersen, H. Eklund
Structures Of Thymidine Kinase 1 Of Human And Mycoplasmic Origin
Proc. Natl. Acad. Sci. Usa V. 101 17970 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
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
8
Ligand/Ion
MAGNESIUM ION
2
TTP
8
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
3
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:153 , CYS A:156 , CYS A:185 , CYS A:188
BINDING SITE FOR RESIDUE ZN A 1193
02
AC2
SOFTWARE
CYS B:153 , CYS B:156 , CYS B:185 , CYS B:188
BINDING SITE FOR RESIDUE ZN B 2193
03
AC3
SOFTWARE
CYS C:153 , CYS C:156 , CYS C:185 , CYS C:188
BINDING SITE FOR RESIDUE ZN C 3193
04
AC4
SOFTWARE
CYS D:153 , CYS D:156 , CYS D:185 , CYS D:188
BINDING SITE FOR RESIDUE ZN D 4193
05
AC5
SOFTWARE
CYS E:153 , CYS E:156 , CYS E:185 , CYS E:188
BINDING SITE FOR RESIDUE ZN E 5193
06
AC6
SOFTWARE
CYS F:153 , CYS F:156 , CYS F:185 , CYS F:188
BINDING SITE FOR RESIDUE ZN F 6193
07
AC7
SOFTWARE
CYS G:153 , CYS G:156 , CYS G:185 , CYS G:188
BINDING SITE FOR RESIDUE ZN G 7193
08
AC8
SOFTWARE
CYS H:153 , CYS H:156 , CYS H:185 , CYS H:188
BINDING SITE FOR RESIDUE ZN H 8193
09
AC9
SOFTWARE
SER A:33 , ARG A:60 , TTP A:1195
BINDING SITE FOR RESIDUE MG A 1194
10
BC1
SOFTWARE
SER B:33 , TTP B:2195
BINDING SITE FOR RESIDUE MG B 2194
11
BC2
SOFTWARE
SER C:33 , TTP C:3195 , HOH C:3215
BINDING SITE FOR RESIDUE MG C 3194
12
BC3
SOFTWARE
SER D:33 , TTP D:4195 , HOH D:4229
BINDING SITE FOR RESIDUE MG D 4194
13
BC4
SOFTWARE
SER E:33 , TTP E:5195
BINDING SITE FOR RESIDUE MG E 5194
14
BC5
SOFTWARE
SER F:33 , TTP F:6195
BINDING SITE FOR RESIDUE MG F 6194
15
BC6
SOFTWARE
SER G:33 , TTP G:7195 , HOH G:7228
BINDING SITE FOR RESIDUE MG G 7194
16
BC7
SOFTWARE
SER H:33 , TTP H:8195 , HOH H:8217
BINDING SITE FOR RESIDUE MG H 8194
17
BC8
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 , GLU A:98 , PHE A:101 , LEU A:124 , THR A:127 , PHE A:128 , PHE A:133 , ARG A:165 , VAL A:172 , GLU A:173 , VAL A:174 , ILE A:175 , GLY A:176 , TYR A:181 , MG A:1194 , HOH A:1202 , HOH A:1214 , HOH A:1218
BINDING SITE FOR RESIDUE TTP A 1195
18
BC9
SOFTWARE
MET B:28 , PHE B:29 , SER B:30 , GLY B:31 , LYS B:32 , SER B:33 , ASP B:58 , ARG B:60 , GLU B:98 , PHE B:101 , LEU B:124 , THR B:127 , PHE B:128 , PHE B:133 , THR B:163 , VAL B:172 , GLU B:173 , VAL B:174 , ILE B:175 , GLY B:176 , TYR B:181 , MG B:2194 , HOH B:2226
BINDING SITE FOR RESIDUE TTP B 2195
19
CC1
SOFTWARE
MET C:28 , PHE C:29 , SER C:30 , GLY C:31 , LYS C:32 , SER C:33 , ASP C:58 , ARG C:60 , GLU C:98 , PHE C:101 , LEU C:124 , THR C:127 , PHE C:128 , PHE C:133 , THR C:163 , ARG C:165 , VAL C:172 , GLU C:173 , VAL C:174 , ILE C:175 , GLY C:176 , TYR C:181 , MG C:3194 , HOH C:3200 , HOH C:3207 , HOH C:3215
BINDING SITE FOR RESIDUE TTP C 3195
20
CC2
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 , ARG D:165 , VAL D:172 , GLU D:173 , VAL D:174 , GLY D:176 , TYR D:181 , MG D:4194 , HOH D:4212 , HOH D:4225 , HOH D:4229 , HOH D:4230
BINDING SITE FOR RESIDUE TTP D 4195
21
CC3
SOFTWARE
MET E:28 , PHE E:29 , SER E:30 , GLY E:31 , LYS E:32 , SER E:33 , ASP E:58 , ARG E:60 , GLU E:98 , PHE E:101 , LEU E:124 , THR E:127 , PHE E:128 , PHE E:133 , ARG E:165 , VAL E:172 , GLU E:173 , VAL E:174 , ILE E:175 , GLY E:176 , TYR E:181 , MG E:5194 , HOH E:5214 , HOH E:5215
BINDING SITE FOR RESIDUE TTP E 5195
22
CC4
SOFTWARE
MET F:28 , PHE F:29 , SER F:30 , GLY F:31 , LYS F:32 , SER F:33 , ASP F:58 , ARG F:60 , PHE F:101 , LEU F:124 , THR F:127 , PHE F:128 , PHE F:133 , THR F:163 , ARG F:165 , VAL F:172 , GLU F:173 , VAL F:174 , ILE F:175 , GLY F:176 , TYR F:181 , MG F:6194 , HOH F:6210 , HOH F:6219 , HOH F:6220
BINDING SITE FOR RESIDUE TTP F 6195
23
CC5
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 , ARG G:165 , VAL G:172 , GLU G:173 , VAL G:174 , GLY G:176 , TYR G:181 , MG G:7194 , HOH G:7202 , HOH G:7214 , HOH G:7216 , HOH G:7228
BINDING SITE FOR RESIDUE TTP G 7195
24
CC6
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 , ARG H:165 , VAL H:172 , GLU H:173 , VAL H:174 , ILE H:175 , GLY H:176 , TYR H:181 , MG H:8194 , HOH H:8204 , HOH H:8205 , HOH H:8208
BINDING SITE FOR RESIDUE TTP H 8195
[
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:172-191 | 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:33-64
H:33-61
28
28
28
30
28
28
32
29
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:74-101
H:75-101
27
27
27
27
27
27
28
27
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:172-191
C:172-191
D:172-191
E:172-191
F:172-192
G:172-191
H:172-191
20
20
20
20
20
21
20
20
[
close EXON info
]
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1xbta1 (A:18-150)
1b: SCOP_d1xbtb1 (B:18-150)
1c: SCOP_d1xbtc1 (C:18-150)
1d: SCOP_d1xbtd1 (D:18-150)
1e: SCOP_d1xbte1 (E:18-150)
1f: SCOP_d1xbtf1 (F:18-150)
1g: SCOP_d1xbtg1 (G:18-150)
1h: SCOP_d1xbth1 (H:18-150)
2a: SCOP_d1xbta2 (A:151-191)
2b: SCOP_d1xbtb2 (B:151-191)
2c: SCOP_d1xbtc2 (C:151-191)
2d: SCOP_d1xbtd2 (D:151-191)
2e: SCOP_d1xbte2 (E:151-191)
2f: SCOP_d1xbtf2 (F:151-191)
2g: SCOP_d1xbtg2 (G:151-191)
2h: SCOP_d1xbth2 (H:151-191)
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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
d1xbta1
A:18-150
1b
d1xbtb1
B:18-150
1c
d1xbtc1
C:18-150
1d
d1xbtd1
D:18-150
1e
d1xbte1
E:18-150
1f
d1xbtf1
F:18-150
1g
d1xbtg1
G:18-150
1h
d1xbth1
H: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
d1xbta2
A:151-191
2b
d1xbtb2
B:151-191
2c
d1xbtc2
C:151-191
2d
d1xbtd2
D:151-191
2e
d1xbte2
E:151-191
2f
d1xbtf2
F:151-191
2g
d1xbtg2
G:151-191
2h
d1xbth2
H:151-191
[
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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_1xbtH01 (H:19-189)
1b: PFAM_TK_1xbtH02 (H:19-189)
1c: PFAM_TK_1xbtH03 (H:19-189)
1d: PFAM_TK_1xbtH04 (H:19-189)
1e: PFAM_TK_1xbtH05 (H:19-189)
1f: PFAM_TK_1xbtH06 (H:19-189)
1g: PFAM_TK_1xbtH07 (H:19-189)
1h: PFAM_TK_1xbtH08 (H:19-189)
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Clan
:
P-loop_NTPase
(1112)
Family
:
TK
(9)
Homo sapiens (Human)
(3)
1a
TK-1xbtH01
H:19-189
1b
TK-1xbtH02
H:19-189
1c
TK-1xbtH03
H:19-189
1d
TK-1xbtH04
H:19-189
1e
TK-1xbtH05
H:19-189
1f
TK-1xbtH06
H:19-189
1g
TK-1xbtH07
H:19-189
1h
TK-1xbtH08
H:19-189
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Asym.Unit (220 KB)
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