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1GX1
Asym. Unit
Info
Asym.Unit (88 KB)
Biol.Unit 1 (81 KB)
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(1)
Title
:
STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
Authors
:
L. E. Kemp, C. S. Bond, W. N. Hunter
Date
:
26 Mar 02 (Deposition) - 03 Apr 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Synthase, Isoprenoid, Lyase, Isoprene Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. E. Kemp, C. S. Bond, W. N. Hunter
Structure Of 2C-Methyl-D-Erythritol 2, 4- Cyclodiphosphate Synthase: An Essential Enzyme For Isoprenoid Biosynthesis And Target For Antimicrobial Drug Development
Proc. Natl. Acad. Sci. Usa V. 99 6591 2002
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Hetero Components
(5, 22)
Info
All Hetero Components
1a: CYTIDINE-5'-DIPHOSPHATE (CDPa)
1b: CYTIDINE-5'-DIPHOSPHATE (CDPb)
1c: CYTIDINE-5'-DIPHOSPHATE (CDPc)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
3a: SELENOMETHIONINE (MSEa)
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)
4a: SULFATE ION (SO4a)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CDP
3
Ligand/Ion
CYTIDINE-5'-DIPHOSPHATE
2
MN
3
Ligand/Ion
MANGANESE (II) ION
3
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
1
Ligand/Ion
SULFATE ION
5
ZN
3
Ligand/Ion
ZINC ION
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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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:8 , HIS A:10 , HIS A:42 , CDP B:1157
BINDING SITE FOR RESIDUE ZN A1157
02
AC2
SOFTWARE
GLU A:135 , CDP A:1158 , HOH A:2090 , HOH A:2091 , HOH A:2092
BINDING SITE FOR RESIDUE MN A1159
03
AC3
SOFTWARE
GLU B:135 , CDP B:1157 , HOH B:2100 , HOH B:2101 , HOH B:2102
BINDING SITE FOR RESIDUE MN B1158
04
AC4
SOFTWARE
ASP B:8 , HIS B:10 , HIS B:42 , CDP B:1160
BINDING SITE FOR RESIDUE ZN B1159
05
AC5
SOFTWARE
CDP B:1160 , HOH B:2104 , HOH B:2105 , GLU C:135
BINDING SITE FOR RESIDUE MN B1161
06
AC6
SOFTWARE
GLY A:138 , ARG A:142 , GLY B:138 , ARG B:142 , GLY C:138 , ARG C:142
BINDING SITE FOR RESIDUE SO4 B1162
07
AC7
SOFTWARE
CDP A:1158 , ASP C:8 , HIS C:10 , HIS C:42
BINDING SITE FOR RESIDUE ZN C1157
08
AC8
SOFTWARE
ALA A:100 , PRO A:103 , LYS A:104 , MSE A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , GLU A:135 , MN A:1159 , HOH A:2077 , HOH A:2088 , HOH A:2089 , HOH A:2091 , HOH A:2092 , ASP C:8 , HIS C:10 , HIS C:42 , ASP C:56 , GLY C:58 , ZN C:1157
BINDING SITE FOR RESIDUE CDP A1158
09
AC9
SOFTWARE
ASP A:8 , HIS A:10 , HIS A:42 , ASP A:56 , GLY A:58 , ZN A:1157 , HOH A:2031 , ALA B:100 , PRO B:103 , LYS B:104 , MSE B:105 , LEU B:106 , ALA B:131 , THR B:132 , THR B:133 , GLU B:135 , MN B:1158 , HOH B:2087 , HOH B:2098 , HOH B:2099 , HOH B:2100 , HOH B:2102
BINDING SITE FOR RESIDUE CDP B1157
10
BC1
SOFTWARE
ASP B:8 , HIS B:10 , HIS B:42 , ASP B:56 , GLY B:58 , ZN B:1159 , MN B:1161 , HOH B:2037 , HOH B:2103 , HOH B:2104 , ALA C:100 , PRO C:103 , LYS C:104 , MSE C:105 , LEU C:106 , ALA C:131 , THR C:132 , THR C:133 , GLU C:135 , HOH C:2093
BINDING SITE FOR RESIDUE CDP B1160
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: ISPF (A:35-50,B:35-50,C:35-50,A:35-50,B:...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISPF
PS01350
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.
ISPF_ECO57
35-50
3
A:35-50
B:35-50
C:35-50
ISPF_SHIFL
35-50
3
A:35-50
B:35-50
C:35-50
ISPF_ECOLI
35-50
3
A:35-50
B:35-50
C:35-50
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Exons
(0, 0)
Info
All Exons
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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, 3)
Info
All SCOP Domains
1a: SCOP_d1gx1a_ (A:)
1b: SCOP_d1gx1b_ (B:)
1c: SCOP_d1gx1c_ (C:)
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Protein Domains
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Organisms
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(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Bacillus chorismate mutase-like
(324)
Superfamily
:
IpsF-like
(56)
Family
:
IpsF-like
(35)
Protein domain
:
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF
(27)
Escherichia coli [TaxId: 562]
(13)
1a
d1gx1a_
A:
1b
d1gx1b_
B:
1c
d1gx1c_
C:
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1gx1A00 (A:0-156)
1b: CATH_1gx1B00 (B:0-156)
1c: CATH_1gx1C00 (C:0-156)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
60s Ribosomal Protein L30; Chain: A;
(235)
Homologous Superfamily
:
[code=3.30.1330.50, no name defined]
(46)
Escherichia coli. Organism_taxid: 511693. Strain: bl21.
(3)
1a
1gx1A00
A:0-156
1b
1gx1B00
B:0-156
1c
1gx1C00
C:0-156
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Pfam Domains
(0, 0)
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all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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