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1H48
Biol. Unit 1
Info
Asym.Unit (166 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (80 KB)
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(1)
Title
:
THE STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE IN COMPLEX WITH CMP AND PRODUCT
Authors
:
L. E. Kemp, M. S. Alphey, C. S. Bond, W. N. Hunter
Date
:
24 Feb 03 (Deposition) - 22 Dec 04 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Synthase, Isoprenoid, Lyase, Isoprene Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. E. Kemp, M. S. Alphey, C. S. Bond, M. Ferguson, S. Hecht, A. Bacher, W. Eisenreich, F. Rohdich, W. N. Hunter
The Identification Of Isoprenoids That Bind In The Intersubunit Cavity Of Escherichia Coli 2C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase By Complementary Biophysical Methods
Acta Crystallogr. , Sect. D V. 61 45 2005
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: CYTIDINE-5'-MONOPHOSPHATE (C5Pa)
1b: CYTIDINE-5'-MONOPHOSPHATE (C5Pb)
1c: CYTIDINE-5'-MONOPHOSPHATE (C5Pc)
1d: CYTIDINE-5'-MONOPHOSPHATE (C5Pd)
1e: CYTIDINE-5'-MONOPHOSPHATE (C5Pe)
1f: CYTIDINE-5'-MONOPHOSPHATE (C5Pf)
2a: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODI... (CDIa)
2b: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODI... (CDIb)
2c: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODI... (CDIc)
2d: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODI... (CDId)
2e: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODI... (CDIe)
2f: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODI... (CDIf)
3a: GERANYL DIPHOSPHATE (GPPa)
3b: GERANYL DIPHOSPHATE (GPPb)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C5P
3
Ligand/Ion
CYTIDINE-5'-MONOPHOSPHATE
2
CDI
3
Ligand/Ion
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
3
GPP
1
Ligand/Ion
GERANYL DIPHOSPHATE
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
5
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: CC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:8 , HIS A:10 , HIS A:42 , CDI A:201
BINDING SITE FOR RESIDUE ZN A 900
02
AC2
SOFTWARE
ASP B:8 , HIS B:10 , HIS B:42 , CDI B:902
BINDING SITE FOR RESIDUE ZN B 900
03
AC3
SOFTWARE
ASP C:8 , HIS C:10 , HIS C:42 , CDI C:902
BINDING SITE FOR RESIDUE ZN C 900
04
AC4
SOFTWARE
HIS A:5 , GLU A:149 , GLU B:149 , HIS C:5 , GLU C:149 , HOH C:1001
BINDING SITE FOR RESIDUE MN C 902
05
AC9
SOFTWARE
ASP A:8 , HIS A:10 , ALA A:33 , HIS A:34 , SER A:35 , HIS A:42 , ILE A:57 , PHE A:61 , ASP A:63 , ZN A:202 , C5P B:901 , GLU B:135
BINDING SITE FOR RESIDUE CDI A 421
06
BC1
SOFTWARE
ASP A:56 , GLY A:58 , CDI A:201 , HOH A:308 , ALA B:100 , PRO B:103 , LYS B:104 , MET B:105 , LEU B:106 , ALA B:131 , THR B:132 , THR B:133 , GLU B:135
BINDING SITE FOR RESIDUE C5P A 901
07
BC2
SOFTWARE
ASP B:8 , HIS B:10 , HIS B:34 , SER B:35 , HIS B:42 , ILE B:57 , PHE B:61 , ZN B:903 , C5P C:901 , GLU C:135
BINDING SITE FOR RESIDUE CDI B 421
08
BC3
SOFTWARE
ASP B:56 , GLY B:58 , ASP B:63 , CDI B:902 , HOH B:1001 , ALA C:100 , PRO C:103 , LYS C:104 , MET C:105 , LEU C:106 , ALA C:131 , THR C:132 , THR C:133
BINDING SITE FOR RESIDUE C5P B 901
09
BC4
SOFTWARE
GLU A:135 , ASP C:8 , HIS C:10 , ALA C:33 , HIS C:34 , SER C:35 , HIS C:42 , ILE C:57 , GLY C:58 , PHE C:61 , ASP C:63 , ZN C:903 , C5P A:203 , HOH C:1004 , HOH A:301
BINDING SITE FOR RESIDUE CDI C 421
10
BC5
SOFTWARE
ALA A:100 , PRO A:103 , LYS A:104 , MET A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , GLU A:135 , ASP C:56 , GLY C:58 , LYS C:59 , ASP C:63 , CDI C:902 , HOH C:1004 , HOH A:301
BINDING SITE FOR RESIDUE C5P C 901
11
CC3
SOFTWARE
PHE A:7 , GLY A:138 , PHE A:139 , THR A:140 , ARG A:142 , GLU A:149 , PHE B:7 , GLY B:138 , PHE B:139 , THR B:140 , ARG B:142 , PHE C:7 , GLY C:138 , PHE C:139 , THR C:140 , ARG C:142 , GLU C:149 , HOH C:1001
BINDING SITE FOR RESIDUE GPP G 903
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 9)
Info
All PROSITE Patterns/Profiles
1: ISPF (A:35-50,B:35-50,C: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_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
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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, 6)
Info
All SCOP Domains
1a: SCOP_d1h48a_ (A:)
1b: SCOP_d1h48b_ (B:)
1c: SCOP_d1h48c_ (C:)
1d: SCOP_d1h48d_ (D:)
1e: SCOP_d1h48e_ (E:)
1f: SCOP_d1h48f_ (F:)
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)
Protein Domains
(
)
(
)
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 [TaxId: 562]
(13)
1a
d1h48a_
A:
1b
d1h48b_
B:
1c
d1h48c_
C:
1d
d1h48d_
D:
1e
d1h48e_
E:
1f
d1h48f_
F:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1h48A00 (A:0-156)
1b: CATH_1h48E00 (E:0-156)
1c: CATH_1h48B00 (B:-1-156)
1d: CATH_1h48D00 (D:-1-156)
1e: CATH_1h48C00 (C:-1-157)
1f: CATH_1h48F00 (F:-1-157)
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Homologous Superfamilies
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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
1h48A00
A:0-156
1b
1h48E00
E:0-156
1c
1h48B00
B:-1-156
1d
1h48D00
D:-1-156
1e
1h48C00
C:-1-157
1f
1h48F00
F:-1-157
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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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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Asym.Unit (166 KB)
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Header - Biol.Unit 1
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