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1T8Q
Biol. Unit 2
Info
Asym.Unit (248 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (123 KB)
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(1)
Title
:
STRUCTURAL GENOMICS, CRYSTAL STRUCTURE OF GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE FROM E. COLI
Authors
:
R. Zhang, Y. Kim, I. Dementieva, N. Duke, L. Stols, M. Donnelly, A. Joach Midwest Center For Structural Genomics (Mcsg)
Date
:
13 May 04 (Deposition) - 03 Aug 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Phosphodiesterase, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Zhang, Y. Kim, I. Dementieva, N. Duke, L. Stols, M. Donnelly, A. Joachimiak
The Crystal Structure Of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
To Be Published
[
close entry info
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Hetero Components
(2, 23)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
5
Ligand/Ion
GLYCEROL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
MSE
18
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(7, 7)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC2 (SOFTWARE)
7: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
GLU B:63 , ASP B:65 , GLU B:171 , GOL B:1606 , HOH B:1612
BINDING SITE FOR RESIDUE MG B 1602
2
AC3
SOFTWARE
GLU C:63 , ASP C:65 , GLU C:171 , GOL C:1607 , HOH C:1614
BINDING SITE FOR RESIDUE MG C 1603
3
AC6
SOFTWARE
HIS B:36 , ARG B:37 , GLU B:63 , ASP B:65 , GLU B:171 , LYS B:173 , PHE B:210 , MG B:1602 , HOH B:1612 , HOH B:1613 , HOH B:1677
BINDING SITE FOR RESIDUE GOL B 1606
4
AC7
SOFTWARE
HIS C:36 , ARG C:37 , GLU C:63 , GLU C:171 , LYS C:173 , PHE C:210 , TYR C:313 , MG C:1603 , HOH C:1653 , HOH C:1739
BINDING SITE FOR RESIDUE GOL C 1607
5
BC1
SOFTWARE
LYS B:195 , HOH B:1847 , HOH B:1870
BINDING SITE FOR RESIDUE GOL B 1610
6
BC2
SOFTWARE
LYS B:140 , LYS C:195 , TYR C:196 , HOH C:1750
BINDING SITE FOR RESIDUE GOL C 1611
7
BC4
SOFTWARE
ARG C:95 , ALA C:96 , ASP C:106 , HOH C:1862
BINDING SITE FOR RESIDUE GOL C 1613
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: GP_PDE (B:31-355,C:31-355)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GP_PDE
PS51704
GP-PDE domain profile.
GLPQ_ECOLI
31-355
2
-
B:31-355
C:31-355
-
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1t8qa_ (A:)
1b: SCOP_d1t8qb_ (B:)
1c: SCOP_d1t8qc_ (C:)
1d: SCOP_d1t8qd_ (D:)
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)
Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLC-like phosphodiesterases
(46)
Family
:
Glycerophosphoryl diester phosphodiesterase
(7)
Protein domain
:
Glycerophosphodiester phosphodiesterase GlpQ
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d1t8qa_
A:
1b
d1t8qb_
B:
1c
d1t8qc_
C:
1d
d1t8qd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1t8qD00 (D:30-356)
1b: CATH_1t8qA00 (A:29-356)
1c: CATH_1t8qC00 (C:29-356)
1d: CATH_1t8qB00 (B:29-357)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphatidylinositol (PI) phosphodiesterase
(37)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1t8qD00
D:30-356
1b
1t8qA00
A:29-356
1c
1t8qC00
C:29-356
1d
1t8qB00
B:29-357
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GDPD_1t8qD01 (D:36-350)
1b: PFAM_GDPD_1t8qD02 (D:36-350)
1c: PFAM_GDPD_1t8qD03 (D:36-350)
1d: PFAM_GDPD_1t8qD04 (D:36-350)
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Clans
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)
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)
Clan
:
PLC
(20)
Family
:
GDPD
(8)
Escherichia coli (strain K12)
(2)
1a
GDPD-1t8qD01
D:36-350
1b
GDPD-1t8qD02
D:36-350
1c
GDPD-1t8qD03
D:36-350
1d
GDPD-1t8qD04
D:36-350
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Chain B
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (248 KB)
Header - Asym.Unit
Biol.Unit 1 (121 KB)
Header - Biol.Unit 1
Biol.Unit 2 (123 KB)
Header - Biol.Unit 2
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