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2V9X
Biol. Unit 1
Info
Asym.Unit (383 KB)
Biol.Unit 1 (186 KB)
Biol.Unit 2 (194 KB)
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(1)
Title
:
E138D VARIANT OF ESCHERICHIA COLI DCTP DEAMINASE IN COMPLEX WITH DUTP
Authors
:
M. Thymark, E. Johansson, S. Larsen, M. Willemoes
Date
:
28 Aug 07 (Deposition) - 20 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,J,K,L (1x)
Biol. Unit 2: D,E,F,G,H,I (1x)
Keywords
:
Dutpase, Hydrolase, Dctp Deaminase, Nucleotide Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Thymark, E. Johansson, S. Larsen, M. Willemoes
Mutational Analysis Of The Nucleotide Binding Site Of Escherichia Coli Dctp Deaminase.
Arch. Biochem. Biophys. V. 470 20 2008
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTa)
1b: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTb)
1c: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTc)
1d: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTd)
1e: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTe)
1f: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTf)
1g: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTg)
1h: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTh)
1i: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTi)
1j: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTj)
1k: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTk)
1l: DEOXYURIDINE-5'-TRIPHOSPHATE (DUTl)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DUT
6
Ligand/Ion
DEOXYURIDINE-5'-TRIPHOSPHATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
SO4
2
Ligand/Ion
SULFATE ION
[
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]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC6 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
13: CC7 (SOFTWARE)
14: CC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:124 , ARG A:126 , ASP A:128 , TRP A:131 , ILE A:135 , VAL A:136 , TYR A:171 , ARG A:174 , ALA A:177 , LYS A:178 , TYR A:179 , GLN A:182 , MG A:1195 , HOH A:2039 , HOH A:2044 , ARG C:110 , SER C:111 , SER C:112 , ARG C:115 , HOH C:2035 , HOH C:2036
BINDING SITE FOR RESIDUE DUT A1194
02
AC2
SOFTWARE
ARG A:110 , SER A:111 , SER A:112 , ARG A:115 , HOH A:2023 , ALA B:124 , ARG B:126 , ASP B:128 , TRP B:131 , ILE B:135 , VAL B:136 , TYR B:171 , ARG B:174 , ALA B:177 , LYS B:178 , GLN B:182 , MG B:1195 , HOH B:2045 , HOH B:2046 , HOH B:2047 , HOH B:2048
BINDING SITE FOR RESIDUE DUT B1194
03
AC3
SOFTWARE
ARG B:110 , SER B:111 , SER B:112 , ARG B:115 , HOH B:2009 , HOH B:2025 , HOH B:2026 , ALA C:124 , ARG C:126 , ASP C:128 , TRP C:131 , ILE C:135 , VAL C:136 , TYR C:171 , ARG C:174 , ALA C:177 , LYS C:178 , TYR C:179 , GLN C:182 , MG C:1195 , HOH C:2052 , HOH C:2053 , HOH C:2054
BINDING SITE FOR RESIDUE DUT C1194
04
AC4
SOFTWARE
ALA J:124 , ARG J:126 , ASP J:128 , TRP J:131 , ILE J:135 , VAL J:136 , TYR J:171 , MG J:1195 , HOH J:2030 , HOH J:2031 , HOH J:2032 , ARG L:110 , SER L:111 , SER L:112 , HOH L:2002
BINDING SITE FOR RESIDUE DUT J1194
05
AC5
SOFTWARE
ARG J:110 , SER J:111 , SER J:112 , ARG J:115 , HOH J:2010 , HOH J:2011 , HOH J:2021 , ALA K:124 , ARG K:126 , ASP K:128 , TRP K:131 , ILE K:135 , VAL K:136 , TYR K:171 , ARG K:174 , ALA K:177 , LYS K:178 , TYR K:179 , GLN K:182 , MG K:1195 , HOH K:2022 , HOH K:2037
BINDING SITE FOR RESIDUE DUT K1194
06
AC6
SOFTWARE
ARG K:110 , SER K:111 , SER K:112 , ARG K:115 , HOH K:2006 , HOH K:2019 , ALA L:124 , ARG L:126 , ASP L:128 , TRP L:131 , ILE L:135 , VAL L:136 , TYR L:171 , MG L:1195 , HOH L:2017 , HOH L:2025
BINDING SITE FOR RESIDUE DUT L1194
07
BC4
SOFTWARE
DUT A:1194 , HOH C:2011
BINDING SITE FOR RESIDUE MG A1195
08
BC5
SOFTWARE
HOH A:2009 , DUT B:1194 , HOH B:2045
BINDING SITE FOR RESIDUE MG B1195
09
BC6
SOFTWARE
HOH B:2009 , DUT C:1194 , HOH C:2052
BINDING SITE FOR RESIDUE MG C1195
10
CC4
SOFTWARE
DUT J:1194 , HOH L:2002
BINDING SITE FOR RESIDUE MG J1195
11
CC5
SOFTWARE
HOH J:2010 , HOH J:2011 , DUT K:1194 , HOH K:2037
BINDING SITE FOR RESIDUE MG K1195
12
CC6
SOFTWARE
HOH K:2006 , DUT L:1194
BINDING SITE FOR RESIDUE MG L1195
13
CC7
SOFTWARE
ARG A:2 , HIS A:125 , ARG B:2 , HIS B:125 , ARG C:2 , HIS C:125
BINDING SITE FOR RESIDUE SO4 C1197
14
CC8
SOFTWARE
LEU K:107 , ASP K:108 , HIS K:121 , HIS K:125 , THR L:123 , HIS L:125
BINDING SITE FOR RESIDUE SO4 K1197
[
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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
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d2v9xa_ (A:)
1b: SCOP_d2v9xe_ (E:)
1c: SCOP_d2v9xf_ (F:)
1d: SCOP_d2v9xg_ (G:)
1e: SCOP_d2v9xh_ (H:)
1f: SCOP_d2v9xi_ (I:)
1g: SCOP_d2v9xj_ (J:)
1h: SCOP_d2v9xk_ (K:)
1i: SCOP_d2v9xl_ (L:)
1j: SCOP_d2v9xb_ (B:)
1k: SCOP_d2v9xc_ (C:)
1l: SCOP_d2v9xd_ (D:)
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(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
dUTPase-like
(122)
Family
:
dUTPase-like
(71)
Protein domain
:
Deoxycytidine triphosphate deaminase (dCTP deaminase)
(9)
Escherichia coli [TaxId: 562]
(6)
1a
d2v9xa_
A:
1b
d2v9xe_
E:
1c
d2v9xf_
F:
1d
d2v9xg_
G:
1e
d2v9xh_
H:
1f
d2v9xi_
I:
1g
d2v9xj_
J:
1h
d2v9xk_
K:
1i
d2v9xl_
L:
1j
d2v9xb_
B:
1k
d2v9xc_
C:
1l
d2v9xd_
D:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_dUTPase_2v9xL01 (L:72-174)
1b: PFAM_dUTPase_2v9xL02 (L:72-174)
1c: PFAM_dUTPase_2v9xL03 (L:72-174)
1d: PFAM_dUTPase_2v9xL04 (L:72-174)
1e: PFAM_dUTPase_2v9xL05 (L:72-174)
1f: PFAM_dUTPase_2v9xL06 (L:72-174)
1g: PFAM_dUTPase_2v9xL07 (L:72-174)
1h: PFAM_dUTPase_2v9xL08 (L:72-174)
1i: PFAM_dUTPase_2v9xL09 (L:72-174)
1j: PFAM_dUTPase_2v9xL10 (L:72-174)
1k: PFAM_dUTPase_2v9xL11 (L:72-174)
1l: PFAM_dUTPase_2v9xL12 (L:72-174)
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Clan
:
dUTPase
(38)
Family
:
dUTPase
(38)
Escherichia coli (strain K12)
(8)
1a
dUTPase-2v9xL01
L:72-174
1b
dUTPase-2v9xL02
L:72-174
1c
dUTPase-2v9xL03
L:72-174
1d
dUTPase-2v9xL04
L:72-174
1e
dUTPase-2v9xL05
L:72-174
1f
dUTPase-2v9xL06
L:72-174
1g
dUTPase-2v9xL07
L:72-174
1h
dUTPase-2v9xL08
L:72-174
1i
dUTPase-2v9xL09
L:72-174
1j
dUTPase-2v9xL10
L:72-174
1k
dUTPase-2v9xL11
L:72-174
1l
dUTPase-2v9xL12
L:72-174
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