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1GTV
Asym. Unit
Info
Asym.Unit (83 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (73 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE-5'-DIPHOSPHATE (TDP)
Authors
:
T. Ursby, M. Weik, E. Fioravanti, M. Delarue, M. Goeldner, D. Bourgeois
Date
:
21 Jan 02 (Deposition) - 28 Mar 02 (Release) - 07 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (2x)
Biol. Unit 2: B (2x)
Keywords
:
Transferase, Transferase (Atp:Tmp Phosphotransferase), Kinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Ursby, M. Weik, E. Fioravanti, M. Delarue, M. Goeldner, D. Bourgeois
Cryophotolysis Of Caged Compounds: A Technique For Trapping Intermediate States In Protein Crystals
Acta Crystallogr. , Sect. D V. 58 607 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 16)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
4a: THYMIDINE-5'-PHOSPHATE (TMPa)
5a: THYMIDINE-5'-DIPHOSPHATE (TYDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
6
Ligand/Ion
ACETATE ION
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
SO4
6
Ligand/Ion
SULFATE ION
4
TMP
1
Ligand/Ion
THYMIDINE-5'-PHOSPHATE
5
TYD
1
Ligand/Ion
THYMIDINE-5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:9 , GLU A:166 , TYD A:302 , HOH A:2193 , HOH A:2244 , ASP B:9 , GLU B:166 , TMP B:302 , HOH B:2029
BINDING SITE FOR RESIDUE MG A 301
02
AC2
SOFTWARE
GLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , ARG A:14 , ARG A:153 , GLY B:10 , ALA B:11 , GLY B:12 , LYS B:13 , ARG B:14 , ARG B:153 , SO4 B:303 , HOH B:2017 , HOH B:2019 , HOH B:2031 , HOH B:2032 , HOH B:2033
BINDING SITE FOR RESIDUE SO4 A 303
03
AC3
SOFTWARE
GLN A:121 , LYS A:132 , ALA A:154 , ALA A:161 , ARG A:162 , ARG A:167 , TRP A:187 , GLY A:188 , GLN B:121 , LYS B:132 , ALA B:154 , ARG B:162 , ARG B:167 , TRP B:187 , GLY B:188 , SO4 B:304 , HOH B:2034
BINDING SITE FOR RESIDUE SO4 A 304
04
AC4
SOFTWARE
TYR A:39 , ALA A:49 , HIS A:53 , TYD A:302 , TYR B:39 , ALA B:49 , HIS B:53 , ACT B:305
BINDING SITE FOR RESIDUE ACT A 305
05
AC5
SOFTWARE
GLU A:55 , HIS A:56 , TRP A:119 , ARG A:122 , ILE A:123 , ARG A:127 , HOH A:2078 , HOH A:2249 , GLU B:55 , HIS B:56 , TRP B:119 , ARG B:122 , ILE B:123 , ARG B:127 , SO4 B:306
BINDING SITE FOR RESIDUE SO4 A 306
06
AC6
SOFTWARE
ASP A:46 , ARG A:127 , HOH A:2250 , ASP B:46 , ARG B:127 , ACT B:307
BINDING SITE FOR RESIDUE ACT A 307
07
AC7
SOFTWARE
ARG A:25 , SER A:30 , VAL A:31 , ARG B:25 , SER B:30 , VAL B:31 , ACT B:308
BINDING SITE FOR RESIDUE ACT A 308
08
AC8
SOFTWARE
ASP A:9 , GLU A:166 , TYD A:302 , HOH A:2193 , HOH A:2244 , ASP B:9 , GLU B:166 , TMP B:302 , HOH B:2029
BINDING SITE FOR RESIDUE MG B 301
09
AC9
SOFTWARE
GLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , ARG A:14 , ARG A:153 , SO4 A:303 , GLY B:10 , ALA B:11 , GLY B:12 , LYS B:13 , ARG B:14 , ARG B:153 , HOH B:2017 , HOH B:2019 , HOH B:2031 , HOH B:2032 , HOH B:2033
BINDING SITE FOR RESIDUE SO4 B 303
10
BC1
SOFTWARE
GLN A:121 , LYS A:132 , ALA A:154 , ALA A:161 , ARG A:162 , ARG A:167 , TRP A:187 , GLY A:188 , SO4 A:304 , GLN B:121 , LYS B:132 , ALA B:154 , ALA B:161 , ARG B:162 , ARG B:167 , TRP B:187 , GLY B:188 , HOH B:2034
BINDING SITE FOR RESIDUE SO4 B 304
11
BC2
SOFTWARE
TYR A:39 , TYD A:302 , ACT A:305 , HOH B:2010 , HOH B:2011
BINDING SITE FOR RESIDUE ACT B 305
12
BC3
SOFTWARE
GLU A:55 , HIS A:56 , TRP A:119 , ARG A:122 , ILE A:123 , ARG A:127 , SO4 A:306 , HOH A:2078 , HOH A:2249 , GLU B:55 , HIS B:56 , TRP B:119 , ARG B:122 , ILE B:123 , ARG B:127
BINDING SITE FOR RESIDUE SO4 B 306
13
BC4
SOFTWARE
ASP A:46 , ARG A:127 , ACT A:307 , HOH A:2250 , ASP B:46 , ARG B:127
BINDING SITE FOR RESIDUE ACT B 307
14
BC5
SOFTWARE
ARG A:25 , SER A:30 , VAL A:31 , ACT A:308 , ARG B:25 , SER B:30 , VAL B:31
BINDING SITE FOR RESIDUE ACT B 308
15
BC6
SOFTWARE
ASP A:9 , PRO A:37 , TYR A:39 , PHE A:70 , ARG A:74 , ARG A:95 , ASN A:100 , TYR A:103 , TYR A:165 , GLU A:166 , MG A:301 , ACT A:305 , HOH A:2193 , HOH A:2243 , HOH A:2244 , HOH A:2245 , HOH A:2246 , ASP B:9 , PHE B:36 , PRO B:37 , TYR B:39 , PHE B:70 , ARG B:74 , ARG B:95 , ASN B:100 , TYR B:103 , TYR B:165 , GLU B:166 , MG B:301 , TMP B:302 , ACT B:305 , HOH B:2022 , HOH B:2023 , HOH B:2026 , HOH B:2029 , HOH B:2030 , HOH B:2031
BINDING SITE FOR RESIDUE TYD A 302
16
BC7
SOFTWARE
ASP A:9 , TYR A:39 , PHE A:70 , ARG A:74 , ARG A:95 , ASN A:100 , TYR A:103 , TYR A:165 , MG A:301 , TYD A:302 , HOH A:2046 , HOH A:2193 , HOH A:2243 , HOH A:2244 , ASP B:9 , PRO B:37 , TYR B:39 , PHE B:70 , ARG B:74 , ARG B:95 , ASN B:100 , TYR B:103 , TYR B:165 , MG B:301 , HOH B:2026 , HOH B:2029 , HOH B:2030 , HOH B:2031
BINDING SITE FOR RESIDUE TMP B 302
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: THYMIDYLATE_KINASE (A:92-104,B:92-104,A:92-104,B:92-10...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THYMIDYLATE_KINASE
PS01331
Thymidylate kinase signature.
KTHY_MYCTO
92-104
2
A:92-104
B:92-104
KTHY_MYCTU
92-104
2
A:92-104
B:92-104
[
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1gtva_ (A:)
1b: SCOP_d1gtvb_ (B:)
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Classes
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(
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(
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(
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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
:
Nucleotide and nucleoside kinases
(231)
Protein domain
:
Thymidylate kinase
(34)
Mycobacterium tuberculosis [TaxId: 1773]
(9)
1a
d1gtva_
A:
1b
d1gtvb_
B:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1gtvA00 (A:1-208)
1b: CATH_1gtvB00 (B:1-208)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(15)
1a
1gtvA00
A:1-208
1b
1gtvB00
B:1-208
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Protein & NOT Site
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Asymmetric Unit 1
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