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1T8Q
Asym. Unit
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
[
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Hetero Components
(3, 51)
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
11
Ligand/Ion
GLYCEROL
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
MSE
36
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:63 , ASP A:65 , GLU A:171 , GOL A:1605 , HOH A:1615
BINDING SITE FOR RESIDUE MG A 1601
02
AC2
SOFTWARE
GLU B:63 , ASP B:65 , GLU B:171 , GOL B:1606 , HOH B:1612
BINDING SITE FOR RESIDUE MG B 1602
03
AC3
SOFTWARE
GLU C:63 , ASP C:65 , GLU C:171 , GOL C:1607 , HOH C:1614
BINDING SITE FOR RESIDUE MG C 1603
04
AC4
SOFTWARE
GLU D:63 , ASP D:65 , GLU D:171 , GOL D:1608 , HOH D:1616
BINDING SITE FOR RESIDUE MG D 1604
05
AC5
SOFTWARE
HIS A:36 , ARG A:37 , GLU A:63 , ASP A:65 , GLU A:171 , LYS A:173 , TYR A:313 , MG A:1601 , HOH A:1615 , HOH A:1616 , HOH A:1657 , HOH A:1905
BINDING SITE FOR RESIDUE GOL A 1605
06
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
07
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
08
AC8
SOFTWARE
HIS D:36 , ARG D:37 , GLU D:63 , ASP D:65 , GLU D:171 , LYS D:173 , PHE D:210 , MG D:1604 , HOH D:1616 , HOH D:1639 , HOH D:1746
BINDING SITE FOR RESIDUE GOL D 1608
09
AC9
SOFTWARE
LYS A:195 , HOH A:1811 , HOH A:1955 , HOH A:1962
BINDING SITE FOR RESIDUE GOL A 1609
10
BC1
SOFTWARE
LYS B:195 , HOH B:1847 , HOH B:1870
BINDING SITE FOR RESIDUE GOL B 1610
11
BC2
SOFTWARE
LYS B:140 , LYS C:195 , TYR C:196 , HOH C:1750
BINDING SITE FOR RESIDUE GOL C 1611
12
BC3
SOFTWARE
LYS D:195 , TYR D:196
BINDING SITE FOR RESIDUE GOL D 1612
13
BC4
SOFTWARE
ARG C:95 , ALA C:96 , ASP C:106 , HOH C:1862
BINDING SITE FOR RESIDUE GOL C 1613
14
BC5
SOFTWARE
ARG A:95 , ASP A:106 , HOH A:1779 , HOH A:1909 , HOH A:1910
BINDING SITE FOR RESIDUE GOL A 1614
15
BC6
SOFTWARE
ARG D:95 , ARG D:97 , ASP D:106 , HOH D:1728 , HOH D:1736
BINDING SITE FOR RESIDUE GOL D 1615
[
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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, 4)
Info
All PROSITE Patterns/Profiles
1: GP_PDE (A:31-355,B:31-355,C:31-355,D:31-35...)
;
View:
Select:
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
4
A:31-355
B:31-355
C:31-355
D: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.
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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(
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Protein Domains
(
)
(
)
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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Topologies
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Homologous Superfamilies
(
)
(
)
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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)
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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Asymmetric Unit 1
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