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3LV8
Biol. Unit 1
Info
Asym.Unit (86 KB)
Biol.Unit 1 (154 KB)
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(1)
Title
:
1.8 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A THYMIDYLATE KINASE (TMK) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 IN COMPLEX WITH TMP, THYMIDINE-5'-DIPHOSPHATE AND ADP
Authors
:
A. S. Halavaty, G. Minasov, I. Dubrovska, J. Winsor, L. Shuvalova, K. Kw W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date
:
19 Feb 10 (Deposition) - 02 Mar 10 (Release) - 18 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Thymidylate Kinase, Vibrio Cholerae, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Atp-Binding, Kinase, Nucleotide Biosynthesis, Nucleotide-Binding, Transferase, Csgid
(Keyword Search:
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Reference
:
A. S. Halavaty, G. Minasov, I. Dubrovska, J. Winsor, L. Shuvalova, K. Kwon, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 8 Angstrom Resolution Crystal Structure Of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 In Complex With Tmp, Thymidine-5'-Diphosphate And Ad
To Be Published
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
3a: CHLORIDE ION (CLa)
4a: THYMIDINE-5'-PHOSPHATE (TMPa)
5a: THYMIDINE-5'-DIPHOSPHATE (TYDa)
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No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
TMP
2
Ligand/Ion
THYMIDINE-5'-PHOSPHATE
5
TYD
2
Ligand/Ion
THYMIDINE-5'-DIPHOSPHATE
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Sites
(10, 10)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:13 , ALA A:14 , GLY A:15 , LYS A:16 , SER A:17 , ARG A:147 , GLN A:189 , SER A:190 , ILE A:191 , VAL A:194 , CA A:217 , HOH A:251 , HOH A:265 , HOH A:284 , HOH A:285 , HOH A:286 , HOH A:381 , HOH A:478 , HOH A:483
BINDING SITE FOR RESIDUE ADP A 213
02
AC2
SOFTWARE
GLU A:12 , GLU A:40 , PRO A:41 , ARG A:51 , LYS A:55 , ARG A:76 , ARG A:98 , SER A:102 , SER A:103 , TYR A:106 , GLN A:107 , ILE A:157 , CA A:218 , HOH A:327 , HOH A:353 , HOH A:381 , HOH A:477
BINDING SITE FOR RESIDUE TMP A 214
03
AC3
SOFTWARE
GLU A:12 , GLU A:40 , ARG A:51 , LYS A:55 , VAL A:72 , ARG A:76 , ARG A:98 , SER A:102 , SER A:103 , TYR A:106 , GLN A:107 , GLU A:158 , CA A:217 , CA A:218 , HOH A:230 , HOH A:265 , HOH A:327 , HOH A:353 , HOH A:381 , HOH A:434 , HOH A:476 , HOH A:477 , HOH A:490
BINDING SITE FOR RESIDUE TYD A 215
04
AC4
SOFTWARE
GLU A:92 , HOH A:314 , HOH A:441 , HOH A:479 , HOH A:480 , HOH A:481 , HOH A:482
BINDING SITE FOR RESIDUE CA A 216
05
AC5
SOFTWARE
ADP A:213 , TYD A:215 , HOH A:265 , HOH A:475 , HOH A:476 , HOH A:477 , HOH A:478
BINDING SITE FOR RESIDUE CA A 217
06
AC6
SOFTWARE
GLU A:12 , GLU A:158 , TMP A:214 , TYD A:215 , HOH A:327 , HOH A:434
BINDING SITE FOR RESIDUE CA A 218
07
AC7
SOFTWARE
ALA A:176 , ASP A:179 , VAL A:182 , HOH A:231 , HOH A:232 , HOH A:392
BINDING SITE FOR RESIDUE CA A 219
08
AC8
SOFTWARE
ASN A:177 , HOH A:267 , HOH A:268 , HOH A:291 , HOH A:292 , HOH A:293
BINDING SITE FOR RESIDUE CA A 220
09
AC9
SOFTWARE
LYS A:130 , HOH A:225 , HOH A:266 , HOH A:328 , HOH A:379
BINDING SITE FOR RESIDUE CA A 221
10
BC1
SOFTWARE
ARG A:111 , HOH A:362 , HOH A:411
BINDING SITE FOR RESIDUE CL A 222
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: THYMIDYLATE_KINASE (A:95-107)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THYMIDYLATE_KINASE
PS01331
Thymidylate kinase signature.
KTHY_VIBCH
95-107
2
A:95-107
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3lv8a_ (A:)
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Protein Domains
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Organisms
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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
:
automated matches
(25)
Vibrio cholerae [TaxId: 243277]
(2)
1a
d3lv8a_
A:
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CATH Domains
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Thymidylate_kin_3lv8A01 (A:8-198)
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Clan
:
P-loop_NTPase
(1112)
Family
:
Thymidylate_kin
(26)
Vibrio cholerae
(2)
1a
Thymidylate_kin-3lv8A01
A:8-198
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