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2YC5
Biol. Unit 1
Info
Asym.Unit (91 KB)
Biol.Unit 1 (165 KB)
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(1)
Title
:
INHIBITORS OF THE HERBICIDAL TARGET ISPD
Authors
:
H. W. Hoeffken
Date
:
11 Mar 11 (Deposition) - 24 Aug 11 (Release) - 24 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Transferase, Non-Mevalonate-Pathway, Herbicide, Allosteric Pocket
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Witschel, H. W. Hoeffken, M. Seet, L. Parra, T. Mietzner, F. Thater, R. Niggeweg, F. Rohl, B. Illarionov, F. Rohdich, J. Kaiser, M. Fischer, A. Bacher, F. Diederich
Inhibitors Of The Herbicidal Target Ispd: Allosteric Site Binding.
Angew. Chem. Int. Ed. Engl. V. 50 7931 2011
(for further references see the
PDB file header
)
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: 5-CHLORO-7-HYDROXY-6-(PHENYLMETHYL... (6BCa)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
3a: CADMIUM ION (CDa)
3b: CADMIUM ION (CDb)
3c: CADMIUM ION (CDc)
4a: COPPER (II) ION (CUa)
4b: COPPER (II) ION (CUb)
4c: COPPER (II) ION (CUc)
5a: MAGNESIUM ION (MGa)
6a: SODIUM ION (NAa)
7a: ZINC ION (ZNa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
6BC
2
Ligand/Ion
5-CHLORO-7-HYDROXY-6-(PHENYLMETHYL)PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
2
ACT
4
Ligand/Ion
ACETATE ION
3
CD
-1
Ligand/Ion
CADMIUM ION
4
CU
-1
Ligand/Ion
COPPER (II) ION
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
NA
-1
Ligand/Ion
SODIUM ION
7
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(12, 12)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:157 , GLN A:158 , ILE A:177 , ALA A:203 , GLN A:238 , VAL A:239 , VAL A:259 , ASP A:261 , ASP A:262 , VAL A:263 , SER A:264 , ILE A:265 , VAL A:266
BINDING SITE FOR RESIDUE 6BC A1300
02
AC2
SOFTWARE
LYS A:123 , GLU A:141 , ASP A:147 , HOH A:2044 , HOH A:2050 , HOH A:2070
BINDING SITE FOR RESIDUE CU A1301
03
AC3
SOFTWARE
LYS A:123 , GLU A:141 , ASP A:147 , HOH A:2044 , HOH A:2050 , HOH A:2070
BINDING SITE FOR RESIDUE CU A1302
04
AC4
SOFTWARE
GLU A:121 , GLU A:191 , HIS A:271 , ACT A:1307
BINDING SITE FOR RESIDUE MG A1303
05
AC5
SOFTWARE
GLU A:167 , HOH A:2065 , HOH A:2066
BINDING SITE FOR RESIDUE CD A1304
06
AC6
SOFTWARE
ASP A:290 , HOH A:2156 , HOH A:2158
BINDING SITE FOR RESIDUE CU A1305
07
AC7
SOFTWARE
LEU A:292 , GLU A:295 , HOH A:2159 , HOH A:2160
BINDING SITE FOR RESIDUE ACT A1306
08
AC8
SOFTWARE
PRO A:120 , GLU A:121 , GLU A:191 , LEU A:244 , HIS A:271 , MG A:1303 , ZN A:1310 , HOH A:2084 , HOH A:2161 , HOH A:2162
BINDING SITE FOR RESIDUE ACT A1307
09
AC9
SOFTWARE
LYS A:214 , ASP A:261 , GLU A:267 , HOH A:2120 , HOH A:2138
BINDING SITE FOR RESIDUE CD A1308
10
BC1
SOFTWARE
ASP A:135
BINDING SITE FOR RESIDUE NA A1309
11
BC2
SOFTWARE
GLU A:121 , GLU A:191 , HIS A:271 , ACT A:1307
BINDING SITE FOR RESIDUE ZN A1310
12
BC3
SOFTWARE
GLU A:138 , GLU A:141 , ASP A:169 , ASN A:171 , HOH A:2036 , HOH A:2045
BINDING SITE FOR RESIDUE CD A1311
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ISPD (A:175-182)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISPD
PS01295
4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.
ISPD_ARATH
175-182
2
A:175-182
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2yc5a_ (A:)
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Protein Domains
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Organisms
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(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
Cytidylytransferase
(43)
Protein domain
:
4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)
(16)
Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702]
(7)
1a
d2yc5a_
A:
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CATH Domains
(0, 0)
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Pfam Domains
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Asym.Unit (91 KB)
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