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1W4R
Asym. Unit
Info
Asym.Unit (244 KB)
Biol.Unit 1 (122 KB)
Biol.Unit 2 (118 KB)
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(1)
Title
:
STRUCTURE OF A TYPE II THYMIDINE KINASE WITH BOUND DTTP
Authors
:
M. S. Birringer, M. T. Claus, G. Folkers, D. P. Kloer, G. E. Schulz, L. Sc
Date
:
27 Jul 04 (Deposition) - 01 Feb 05 (Release) - 06 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.83
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
:
Transferase, Type Ii, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Birringer, M. T. Claus, G. Folkers, D. P. Kloer, G. E. Schulz, L. Scapozza
Structure Of A Type Ii Thymidine Kinase With Bound Dttp
Febs Lett. V. 579 1376 2005
[
close entry info
]
Hetero Components
(3, 17)
Info
All Hetero Components
1a: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTUa)
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
DTU
1
Ligand/Ion
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
2
TTP
8
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
3
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
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 400
02
AC2
SOFTWARE
CYS B:153 , CYS B:156 , CYS B:185 , CYS B:188
BINDING SITE FOR RESIDUE ZN B 400
03
AC3
SOFTWARE
CYS C:153 , CYS C:156 , CYS C:185 , CYS C:188
BINDING SITE FOR RESIDUE ZN C 400
04
AC4
SOFTWARE
CYS D:153 , CYS D:156 , CYS D:185 , CYS D:188
BINDING SITE FOR RESIDUE ZN D 400
05
AC5
SOFTWARE
CYS E:153 , CYS E:156 , CYS E:185 , CYS E:188
BINDING SITE FOR RESIDUE ZN E 400
06
AC6
SOFTWARE
CYS F:153 , CYS F:156 , CYS F:185 , CYS F:188
BINDING SITE FOR RESIDUE ZN F 400
07
AC7
SOFTWARE
CYS G:153 , CYS G:156 , CYS G:185 , CYS G:188
BINDING SITE FOR RESIDUE ZN G 400
08
AC8
SOFTWARE
CYS H:153 , CYS H:156 , CYS H:185 , CYS H:188
BINDING SITE FOR RESIDUE ZN H 400
09
AC9
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 , VAL A:172 , GLU A:173 , VAL A:174 , ILE A:175 , GLY A:176 , TYR A:181 , HOH A:2104 , HOH A:2105 , HOH A:2108 , HOH A:2109 , HOH A:2110
BINDING SITE FOR RESIDUE TTP A 300
10
BC1
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 , ARG B:165 , VAL B:172 , GLU B:173 , VAL B:174 , ILE B:175 , GLY B:176 , TYR B:181 , HOH B:2034 , HOH B:2100 , HOH B:2102 , HOH B:2103 , HOH B:2104 , HOH B:2105 , HOH B:2106 , HOH B:2107 , HOH B:2108
BINDING SITE FOR RESIDUE TTP B 300
11
BC2
SOFTWARE
PRO C:27 , 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 , ARG C:165 , VAL C:172 , GLU C:173 , VAL C:174 , ILE C:175 , GLY C:176 , TYR C:181 , HOH C:2080 , HOH C:2081 , HOH C:2083 , HOH C:2084 , HOH C:2085
BINDING SITE FOR RESIDUE TTP C 300
12
BC3
SOFTWARE
MET D:28 , SER D:30 , GLY D:31 , LYS D:32 , SER D:33 , ASP D:58 , ARG D:60 , ASP D:97 , GLU D:98 , GLN D:100 , PHE D:101 , LEU D:124 , THR D:127 , PHE D:128 , PHE D:133 , VAL D:172 , GLU D:173 , VAL D:174 , ILE D:175 , GLY D:176 , TYR D:181 , HOH D:2088 , HOH D:2089 , HOH D:2090 , HOH D:2092 , HOH D:2093 , HOH D:2094 , HOH D:2095
BINDING SITE FOR RESIDUE TTP D 300
13
BC4
SOFTWARE
MET E:28 , GLY E:31 , LYS E:32 , SER E:33 , ASP E:58 , ASP E:97 , GLU E:98 , GLN E:100 , 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 , HOH E:2075 , HOH E:2076 , HOH E:2077 , HOH E:2078 , HOH E:2079 , HOH E:2080 , HOH E:2081
BINDING SITE FOR RESIDUE TTP E 300
14
BC5
SOFTWARE
ARG B:82 , ASP B:104 , GLU B:107 , ALA B:111 , GLU E:110 , ALA E:111 , ASN E:114 , HOH E:2082 , HOH E:2083
BINDING SITE FOR RESIDUE DTU E1193
15
BC6
SOFTWARE
MET F:28 , SER F:30 , GLY F:31 , LYS F:32 , SER F:33 , ASP F:58 , ARG F:60 , ASP F:97 , GLU F:98 , GLN F:100 , PHE F:101 , LEU F:124 , THR F:127 , PHE F:128 , PHE F:133 , VAL F:172 , GLU F:173 , VAL F:174 , ILE F:175 , GLY F:176 , TYR F:181 , HOH F:2109 , HOH F:2110 , HOH F:2111 , HOH F:2112 , HOH F:2113 , HOH F:2115 , HOH F:2116 , HOH F:2117
BINDING SITE FOR RESIDUE TTP F 300
16
BC7
SOFTWARE
MET G:28 , SER G:30 , GLY G:31 , LYS G:32 , SER G:33 , ASP G:58 , ARG G:60 , ASP G:97 , GLU G:98 , GLN G:100 , PHE G:101 , LEU G:124 , THR G:127 , PHE G:128 , PHE G:133 , VAL G:172 , GLU G:173 , VAL G:174 , ILE G:175 , GLY G:176 , TYR G:181 , HOH G:2100 , HOH G:2101 , HOH G:2102 , HOH G:2103 , HOH G:2106 , HOH G:2107 , HOH G:2108
BINDING SITE FOR RESIDUE TTP G 300
17
BC8
SOFTWARE
MET H:28 , GLY H:31 , LYS H:32 , SER H:33 , ASP H:58 , ARG H:60 , ASP H:97 , GLU H:98 , GLN H:100 , 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 , HOH H:2081 , HOH H:2082 , HOH H:2083 , HOH H:2084 , HOH H:2085 , HOH H:2086 , HOH H:2087 , HOH H:2088
BINDING SITE FOR RESIDUE TTP H 300
[
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:33-70 | B:33-65 | C:33-60 | D:33...)
Exon 1.4 (A:70-101 | B:73-101 | 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:33-70
B:33-65
C:33-60
D:33-60
E:33-60
F:33-61
G:33-60
H:33-60
38
33
28
28
28
29
28
28
1.4
ENST00000301634
4
ENSE00001118177
chr17:
76178763-76178670
94
KITH_HUMAN
70-101
32
8
A:70-101
B:73-101
C:75-101
D:75-101
E:75-101
F:75-101
G:75-101
H:74-101
32
29
27
27
27
27
27
28
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:172-191
G:172-191
H:172-191
20
20
20
20
20
20
20
20
[
close EXON info
]
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1w4ra1 (A:18-150)
1b: SCOP_d1w4rb1 (B:18-150)
1c: SCOP_d1w4rc1 (C:18-150)
1d: SCOP_d1w4rd1 (D:18-150)
1e: SCOP_d1w4re1 (E:18-150)
1f: SCOP_d1w4rf1 (F:18-150)
1g: SCOP_d1w4rg1 (G:18-150)
1h: SCOP_d1w4rh1 (H:18-150)
2a: SCOP_d1w4ra2 (A:151-191)
2b: SCOP_d1w4rb2 (B:151-191)
2c: SCOP_d1w4rc2 (C:151-191)
2d: SCOP_d1w4rd2 (D:151-191)
2e: SCOP_d1w4re2 (E:151-191)
2f: SCOP_d1w4rf2 (F:151-191)
2g: SCOP_d1w4rg2 (G:151-191)
2h: SCOP_d1w4rh2 (H:151-191)
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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
d1w4ra1
A:18-150
1b
d1w4rb1
B:18-150
1c
d1w4rc1
C:18-150
1d
d1w4rd1
D:18-150
1e
d1w4re1
E:18-150
1f
d1w4rf1
F:18-150
1g
d1w4rg1
G:18-150
1h
d1w4rh1
H: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
d1w4ra2
A:151-191
2b
d1w4rb2
B:151-191
2c
d1w4rc2
C:151-191
2d
d1w4rd2
D:151-191
2e
d1w4re2
E:151-191
2f
d1w4rf2
F:151-191
2g
d1w4rg2
G:151-191
2h
d1w4rh2
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_1w4rH01 (H:19-189)
1b: PFAM_TK_1w4rH02 (H:19-189)
1c: PFAM_TK_1w4rH03 (H:19-189)
1d: PFAM_TK_1w4rH04 (H:19-189)
1e: PFAM_TK_1w4rH05 (H:19-189)
1f: PFAM_TK_1w4rH06 (H:19-189)
1g: PFAM_TK_1w4rH07 (H:19-189)
1h: PFAM_TK_1w4rH08 (H:19-189)
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Clan
:
P-loop_NTPase
(1112)
Family
:
TK
(9)
Homo sapiens (Human)
(3)
1a
TK-1w4rH01
H:19-189
1b
TK-1w4rH02
H:19-189
1c
TK-1w4rH03
H:19-189
1d
TK-1w4rH04
H:19-189
1e
TK-1w4rH05
H:19-189
1f
TK-1w4rH06
H:19-189
1g
TK-1w4rH07
H:19-189
1h
TK-1w4rH08
H:19-189
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