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3ERN
Biol. Unit 2
Info
Asym.Unit (157 KB)
Biol.Unit 1 (78 KB)
Biol.Unit 2 (77 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH ARACMP
Authors
:
W. N. Hunter, N. L. Ramsden, L. A. Kemp
Date
:
02 Oct 08 (Deposition) - 25 Aug 09 (Release) - 25 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Mecdp-Synthase, Isoprene Biosynthesis, Lyase, Magnesium, Manganese, Metal-Binding
(Keyword Search:
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]
)
Reference
:
N. L. Ramsden, L. Buetow, A. Dawson, L. A. Kemp, V. Ulaganathan, R. Brenk, G. Klebe, W. N. Hunter
A Structure-Based Approach To Ligand Discovery For 2C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy
J. Med. Chem. V. 52 2531 2009
(for further references see the
PDB file header
)
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: CYTOSINE ARABINOSE-5'-PHOSPHATE (CARa)
1b: CYTOSINE ARABINOSE-5'-PHOSPHATE (CARb)
1c: CYTOSINE ARABINOSE-5'-PHOSPHATE (CARc)
1d: CYTOSINE ARABINOSE-5'-PHOSPHATE (CARd)
1e: CYTOSINE ARABINOSE-5'-PHOSPHATE (CARe)
2a: GERANYL DIPHOSPHATE (GPPa)
2b: GERANYL DIPHOSPHATE (GPPb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CAR
2
Mod. Residue
CYTOSINE ARABINOSE-5'-PHOSPHATE
2
GPP
1
Ligand/Ion
GERANYL DIPHOSPHATE
3
SO4
1
Ligand/Ion
SULFATE ION
4
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(6, 6)
Info
All Sites
1: AC8 (SOFTWARE)
2: AC9 (SOFTWARE)
3: BC1 (SOFTWARE)
4: BC2 (SOFTWARE)
5: BC3 (SOFTWARE)
6: BC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC8
SOFTWARE
ASP D:8 , HIS D:10 , HIS D:42
BINDING SITE FOR RESIDUE ZN D 800
2
AC9
SOFTWARE
ALA D:100 , PRO D:103 , LYS D:104 , MET D:105 , LEU D:106 , ALA D:131 , THR D:132 , THR D:133 , HOH D:903 , HOH D:937 , ASP F:56 , GLY F:58
BINDING SITE FOR RESIDUE CAR D 900
3
BC1
SOFTWARE
ASP D:56 , GLY D:58 , ALA E:100 , PRO E:103 , LYS E:104 , MET E:105 , LEU E:106 , ALA E:131 , THR E:132 , THR E:133 , HOH E:902 , HOH E:916
BINDING SITE FOR RESIDUE CAR E 900
4
BC2
SOFTWARE
ASP E:8 , HIS E:10 , HIS E:42 , SO4 E:801 , HOH E:943
BINDING SITE FOR RESIDUE ZN E 800
5
BC3
SOFTWARE
HIS E:10 , ALA E:33 , HIS E:34 , SER E:35 , HIS E:42 , ZN E:800 , HOH E:943
BINDING SITE FOR RESIDUE SO4 E 801
6
BC4
SOFTWARE
GLY D:138 , PHE D:139 , ARG D:142 , GLY E:138 , PHE E:139 , ARG E:142 , GLU E:149 , GLY F:138 , PHE F:139 , ARG F:142 , GLU F:149 , HOH F:948
BINDING SITE FOR RESIDUE GPP F 902
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: ISPF (D:35-50,E:35-50,F:35-50)
;
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_ECOLI
35-50
3
-
-
-
D:35-50
E:35-50
F:35-50
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Exons
(0, 0)
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3erna_ (A:)
1b: SCOP_d3ernb_ (B:)
1c: SCOP_d3ernc_ (C:)
1d: SCOP_d3ernd_ (D:)
1e: SCOP_d3erne_ (E:)
1f: SCOP_d3ernf_ (F:)
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)
Protein Domains
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)
(
)
Organisms
(
)
(
)
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 K-12 [TaxId: 83333]
(5)
1a
d3erna_
A:
1b
d3ernb_
B:
1c
d3ernc_
C:
1d
d3ernd_
D:
1e
d3erne_
E:
1f
d3ernf_
F:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3ernC00 (C:0-156)
1b: CATH_3ernA00 (A:0-156)
1c: CATH_3ernB00 (B:0-156)
1d: CATH_3ernD00 (D:0-156)
1e: CATH_3ernE00 (E:0-156)
1f: CATH_3ernF00 (F:0-156)
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Organisms
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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 k-12. Organism_taxid: 83333. Strain: k12.
(4)
1a
3ernC00
C:0-156
1b
3ernA00
A:0-156
1c
3ernB00
B:0-156
1d
3ernD00
D:0-156
1e
3ernE00
E:0-156
1f
3ernF00
F:0-156
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (157 KB)
Header - Asym.Unit
Biol.Unit 1 (78 KB)
Header - Biol.Unit 1
Biol.Unit 2 (77 KB)
Header - Biol.Unit 2
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