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3ED0
Asym. Unit
Info
Asym.Unit (163 KB)
Biol.Unit 1 (158 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABZ) FROM HELICOBACTER PYLORI IN COMPLEX WITH EMODIN
Authors
:
L. Zhang, H. Zhang, W. Liu, Y. Guo, X. Shen, H. Jiang
Date
:
02 Sep 08 (Deposition) - 21 Jul 09 (Release) - 21 Jul 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Fabz Complex, Emodin, Cytoplasm, Lipid A Biosynthesis, Lipid Synthesis, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Chen, L. Zhang, Y. Zhang, H. Zhang, J. Du, J. Ding, Y. Guo, H. Jiang, X. Shen
Emodin Targets The Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase From Helicobacter Pylori: Enzymatic Inhibition Assay With Crystal Structural And Thermodynamic Characterization
Bmc Microbiol. V. 9 91 2009
(for further references see the
PDB file header
)
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: BENZAMIDINE (BENa)
1b: BENZAMIDINE (BENb)
1c: BENZAMIDINE (BENc)
1d: BENZAMIDINE (BENd)
1e: BENZAMIDINE (BENe)
1f: BENZAMIDINE (BENf)
1g: BENZAMIDINE (BENg)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUI... (EMOa)
3b: 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUI... (EMOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BEN
7
Ligand/Ion
BENZAMIDINE
2
CL
6
Ligand/Ion
CHLORIDE ION
3
EMO
2
Ligand/Ion
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
[
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:40 , GLU A:124 , VAL A:125 , THR E:138 , GLU E:148 , BEN E:161
BINDING SITE FOR RESIDUE BEN A 160
02
AC2
SOFTWARE
MET A:131 , MET A:154 , ILE A:155 , LEU F:86 , ASP F:90 , ILE F:93
BINDING SITE FOR RESIDUE BEN A 161
03
AC3
SOFTWARE
HIS A:58 , GLY A:67 , EMO A:163
BINDING SITE FOR RESIDUE CL A 162
04
AC4
SOFTWARE
PHE A:59 , PHE A:109 , ARG A:110 , ILE A:111 , PRO A:112 , CL A:162 , HOH A:165 , HOH A:226 , HOH A:257 , ILE B:98 , TYR B:100 , HOH B:243
BINDING SITE FOR RESIDUE EMO A 163
05
AC5
SOFTWARE
ILE B:20 , LEU B:21 , HIS B:23 , PHE B:83 , LYS B:97 , ILE B:98 , VAL B:99
BINDING SITE FOR RESIDUE BEN B 160
06
AC6
SOFTWARE
TRP B:87 , GLY B:88 , HOH B:240 , LEU E:86 , GLY E:130
BINDING SITE FOR RESIDUE BEN B 161
07
AC7
SOFTWARE
HOH A:175 , HIS B:58 , GLY B:67
BINDING SITE FOR RESIDUE CL B 162
08
AC8
SOFTWARE
GLY C:67 , HOH D:231
BINDING SITE FOR RESIDUE CL C 160
09
AC9
SOFTWARE
ILE C:20 , LEU C:21 , PRO C:22 , HIS C:23 , ALA C:75 , GLN C:76 , GLY C:79 , PHE C:80 , PHE C:83 , LYS C:97 , ILE C:98 , VAL C:99 , PHE C:101 , ARG C:158 , HOH C:164 , HOH C:226 , HOH C:229 , PHE D:59
BINDING SITE FOR RESIDUE EMO C 161
10
BC1
SOFTWARE
ALA C:38 , THR C:84 , SER C:85 , LEU C:86 , TRP C:87 , GLY C:88 , GLN D:40 , HOH D:212
BINDING SITE FOR RESIDUE BEN D 160
11
BC2
SOFTWARE
GLY D:67
BINDING SITE FOR RESIDUE CL D 161
12
BC3
SOFTWARE
THR A:138 , GLU A:148 , HOH A:222 , GLU E:124 , VAL E:125 , LEU E:126
BINDING SITE FOR RESIDUE BEN E 160
13
BC4
SOFTWARE
BEN A:160 , HOH A:222 , GLY E:136 , GLY E:137 , ALA E:149 , GLU E:150
BINDING SITE FOR RESIDUE BEN E 161
14
BC5
SOFTWARE
GLY E:67 , HOH F:244
BINDING SITE FOR RESIDUE CL E 162
15
BC6
SOFTWARE
HOH E:209 , HIS F:58 , GLY F:67
BINDING SITE FOR RESIDUE CL F 160
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3ed0a_ (A:)
1b: SCOP_d3ed0b_ (B:)
1c: SCOP_d3ed0c_ (C:)
1d: SCOP_d3ed0d_ (D:)
1e: SCOP_d3ed0e_ (E:)
1f: SCOP_d3ed0f_ (F:)
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(
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(
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(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Thioesterase/thiol ester dehydrase-isomerase
(151)
Superfamily
:
Thioesterase/thiol ester dehydrase-isomerase
(151)
Family
:
FabZ-like
(24)
Protein domain
:
(3R)-hydroxymyristoyl ACP dehydrase FabZ
(24)
Helicobacter pylori [TaxId: 210]
(15)
1a
d3ed0a_
A:
1b
d3ed0b_
B:
1c
d3ed0c_
C:
1d
d3ed0d_
D:
1e
d3ed0e_
E:
1f
d3ed0f_
F:
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3ed0F00 (F:11-158)
1b: CATH_3ed0B00 (B:10-159)
1c: CATH_3ed0C00 (C:9-158)
1d: CATH_3ed0E00 (E:9-159)
1e: CATH_3ed0A00 (A:8-159)
1f: CATH_3ed0D00 (D:8-159)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Thiol Ester Dehydrase; Chain A
(90)
Homologous Superfamily
:
[code=3.10.129.10, no name defined]
(90)
Helicobacter pylori. Organism_taxid: 210. Strain: ss1.
(4)
1a
3ed0F00
F:11-158
1b
3ed0B00
B:10-159
1c
3ed0C00
C:9-158
1d
3ed0E00
E:9-159
1e
3ed0A00
A:8-159
1f
3ed0D00
D:8-159
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Pfam Domains
(0, 0)
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Chain F
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
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ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (163 KB)
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