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2GLM
Asym. Unit
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Asym.Unit (167 KB)
Biol.Unit 1 (161 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE(FABZ) FROM HELICOBACTER PYLORI COMPLEXED WITH COMPOUND 2
Authors
:
L. Zhang, W. Liu, X. Shen, H. Jiang
Date
:
05 Apr 06 (Deposition) - 13 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
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. Zhang, W. Liu, T. Hu, L. Du, C. Luo, K. Chen, X. Shen, H. Jiang
Structural Basis For Catalytic And Inhibitory Mechanisms Of Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz).
J. Biol. Chem. V. 283 5370 2008
(for further references see the
PDB file header
)
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Hetero Components
(3, 14)
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: 2-CHLORO-5-(5-{(E)-[(2Z)-3-(2-METH... (SCBa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BEN
7
Ligand/Ion
BENZAMIDINE
2
CL
6
Ligand/Ion
CHLORIDE ION
3
SCB
1
Ligand/Ion
2-CHLORO-5-(5-{(E)-[(2Z)-3-(2-METHOXYETHYL)-4-OXO-2-(PHENYLIMINO)-1,3-THIAZOLIDIN-5-YLIDENE]METHYL}-2-FURYL)BENZOIC ACID
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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
GLY A:67 , SCB A:3001 , HOH A:3102
BINDING SITE FOR RESIDUE CL A 1001
02
AC2
SOFTWARE
HOH A:3009 , HOH A:3047 , HIS B:58 , GLY B:67
BINDING SITE FOR RESIDUE CL B 1002
03
AC3
SOFTWARE
GLY C:67
BINDING SITE FOR RESIDUE CL C 1003
04
AC4
SOFTWARE
HIS D:58 , GLY D:67
BINDING SITE FOR RESIDUE CL D 1004
05
AC5
SOFTWARE
GLY E:67 , PHE F:101
BINDING SITE FOR RESIDUE CL F 1005
06
AC6
SOFTWARE
GLY F:67
BINDING SITE FOR RESIDUE CL F 1006
07
AC7
SOFTWARE
GLN A:40 , GLU A:124 , VAL A:125 , THR E:138 , VAL E:145 , GLU E:148
BINDING SITE FOR RESIDUE BEN A 2002
08
AC8
SOFTWARE
LYS A:106 , GLU A:150 , LEU E:126 , LYS E:127
BINDING SITE FOR RESIDUE BEN A 2003
09
AC9
SOFTWARE
PHE A:59 , PRO A:60 , ASN A:61 , LYS A:62 , ILE A:64 , PRO A:112 , CL A:1001 , HOH A:3084 , PRO B:22 , ILE B:98 , VAL B:99 , TYR B:100 , PHE B:101 , ARG B:158 , HOH B:2003 , HOH B:2055 , HOH B:2088 , HOH B:2089
BINDING SITE FOR RESIDUE SCB A 3001
10
BC1
SOFTWARE
ILE B:20 , LEU B:21 , PRO B:22 , PHE B:83 , ALA B:94 , LYS B:97 , VAL B:99 , ARG B:158 , HOH B:2021 , HOH B:2089
BINDING SITE FOR RESIDUE BEN B 2001
11
BC2
SOFTWARE
ILE C:20 , LEU C:21 , PRO C:22 , HIS C:23 , LYS C:97 , VAL C:99 , HOH C:2062 , HOH C:2077
BINDING SITE FOR RESIDUE BEN C 2004
12
BC3
SOFTWARE
ALA C:38 , THR C:84 , SER C:85 , LEU C:86 , TRP C:87 , GLY C:88 , HOH C:2071 , GLN D:40 , BEN D:2006
BINDING SITE FOR RESIDUE BEN C 2005
13
BC4
SOFTWARE
GLN C:9 , TRP C:87 , GLY C:88 , PHE C:89 , BEN C:2005 , HOH C:2040
BINDING SITE FOR RESIDUE BEN D 2006
14
BC5
SOFTWARE
TRP B:87 , HOH B:2030 , LEU E:86 , TRP E:87 , GLY E:130 , MET E:131 , HOH E:2091
BINDING SITE FOR RESIDUE BEN E 2007
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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
(0, 0)
Info
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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_d2glma_ (A:)
1b: SCOP_d2glmb_ (B:)
1c: SCOP_d2glmc_ (C:)
1d: SCOP_d2glmd_ (D:)
1e: SCOP_d2glme_ (E:)
1f: SCOP_d2glmf_ (F:)
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Classes
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)
(
)
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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
d2glma_
A:
1b
d2glmb_
B:
1c
d2glmc_
C:
1d
d2glmd_
D:
1e
d2glme_
E:
1f
d2glmf_
F:
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2glmF00 (F:11-157)
1b: CATH_2glmB00 (B:9-159)
1c: CATH_2glmC00 (C:9-159)
1d: CATH_2glmA00 (A:8-159)
1e: CATH_2glmD00 (D:8-159)
1f: CATH_2glmE00 (E:8-159)
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Topologies
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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: 102617. Strain: ss1.
(4)
1a
2glmF00
F:11-157
1b
2glmB00
B:9-159
1c
2glmC00
C:9-159
1d
2glmA00
A:8-159
1e
2glmD00
D:8-159
1f
2glmE00
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 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'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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Asym.Unit (167 KB)
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