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3DP0
Asym. Unit
Info
Asym.Unit (161 KB)
Biol.Unit 1 (156 KB)
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Title
:
CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABZ) FROM HELICOBACTER PYLORI IN COMPLEX WITH COMPOUND 3M
Authors
:
L. Zhang, L. He, X. Liu, H. Liu, X. Shen, H. Jiang
Date
:
07 Jul 08 (Deposition) - 05 May 09 (Release) - 30 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Fabz Complex, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. He, L. Zhang, X. Liu, X. Li, M. Zheng, H. Li, K. Yu, K. Chen, X. Shen, H. Jiang, H. Liu
Discovering Potent Inhibitors Against The Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) Of Helicobacter Pylori: Structure-Based Design, Synthesis, Bioassay, And Crystal Structure Determination.
J. Med. Chem. V. 52 2465 2009
(for further references see the
PDB file header
)
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: N'-[(1E)-(3,5-DIBROMO-2,4-DIHYDROX... (2BCa)
2a: BENZAMIDINE (BENa)
2b: BENZAMIDINE (BENb)
2c: BENZAMIDINE (BENc)
2d: BENZAMIDINE (BENd)
2e: BENZAMIDINE (BENe)
2f: BENZAMIDINE (BENf)
2g: BENZAMIDINE (BENg)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2BC
1
Ligand/Ion
N'-[(1E)-(3,5-DIBROMO-2,4-DIHYDROXYPHENYL)METHYLIDENE]NAPHTHALENE-2-CARBOHYDRAZIDE
2
BEN
7
Ligand/Ion
BENZAMIDINE
3
CL
6
Ligand/Ion
CHLORIDE ION
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Sites
(14, 14)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:58 , GLY A:67 , HOH B:172
BINDING SITE FOR RESIDUE CL A 160
02
AC2
SOFTWARE
HOH A:169 , HOH A:175 , GLY B:67
BINDING SITE FOR RESIDUE CL B 160
03
AC3
SOFTWARE
GLY C:67 , HOH D:197
BINDING SITE FOR RESIDUE CL C 160
04
AC4
SOFTWARE
GLY D:67 , HOH D:168
BINDING SITE FOR RESIDUE CL D 160
05
AC5
SOFTWARE
GLY E:67
BINDING SITE FOR RESIDUE CL E 160
06
AC6
SOFTWARE
GLY F:67
BINDING SITE FOR RESIDUE CL F 160
07
AC7
SOFTWARE
MET A:131 , MET A:154 , ILE A:155 , ALA A:156 , LEU F:86 , ASP F:90 , ILE F:93
BINDING SITE FOR RESIDUE BEN A 161
08
AC8
SOFTWARE
ILE B:20 , LEU B:21 , PHE B:83 , ALA B:94 , LYS B:97 , ILE B:98 , VAL B:99
BINDING SITE FOR RESIDUE BEN B 161
09
AC9
SOFTWARE
PHE A:59 , LYS A:62 , PHE A:109 , ARG A:110 , ILE A:111 , ILE B:98 , ARG B:158 , GLU B:159 , HOH B:202 , HOH B:224 , HOH B:226
BINDING SITE FOR RESIDUE 2BC B 162
10
BC1
SOFTWARE
ALA C:38 , THR C:84 , SER C:85 , LEU C:86 , TRP C:87 , GLY C:88 , GLN D:40
BINDING SITE FOR RESIDUE BEN C 161
11
BC2
SOFTWARE
GLN A:40 , GLU A:124 , VAL A:125 , THR E:138 , VAL E:145 , GLU E:148 , BEN E:163
BINDING SITE FOR RESIDUE BEN E 161
12
BC3
SOFTWARE
TRP B:87 , GLY B:88 , HOH B:229 , LEU E:86 , TRP E:87 , GLY E:130 , HOH E:282
BINDING SITE FOR RESIDUE BEN E 162
13
BC4
SOFTWARE
GLU A:150 , GLY E:136 , GLY E:137 , ALA E:149 , GLU E:150 , BEN E:161
BINDING SITE FOR RESIDUE BEN E 163
14
BC5
SOFTWARE
THR A:138 , GLU A:148 , GLN E:40 , GLU E:124 , VAL E:125 , LEU E:126
BINDING SITE FOR RESIDUE BEN E 164
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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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_d3dp0a_ (A:)
1b: SCOP_d3dp0b_ (B:)
1c: SCOP_d3dp0c_ (C:)
1d: SCOP_d3dp0d_ (D:)
1e: SCOP_d3dp0e_ (E:)
1f: SCOP_d3dp0f_ (F:)
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Classes
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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
d3dp0a_
A:
1b
d3dp0b_
B:
1c
d3dp0c_
C:
1d
d3dp0d_
D:
1e
d3dp0e_
E:
1f
d3dp0f_
F:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3dp0F00 (F:11-158)
1b: CATH_3dp0B00 (B:10-159)
1c: CATH_3dp0C00 (C:9-159)
1d: CATH_3dp0A00 (A:8-159)
1e: CATH_3dp0D00 (D:8-159)
1f: CATH_3dp0E00 (E: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)
Campylobacter pylori (Helicobacter pylori)
(7)
1a
3dp0F00
F:11-158
1b
3dp0B00
B:10-159
1c
3dp0C00
C:9-159
1d
3dp0A00
A:8-159
1e
3dp0D00
D:8-159
1f
3dp0E00
E:8-159
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Pfam Domains
(0, 0)
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Chain F
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 (161 KB)
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