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Asym. Unit
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Asym.Unit (122 KB)
Biol.Unit 1 (116 KB)
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(1)
Title
:
STRUCTURE OF AN ENGINEERED ORGANOPHOSPHOROUS HYDROLASE WITH INCREASED ACTIVITY TOWARD HYDROLYSIS OF PHOSPHOTHIOLATE BONDS
Authors
:
A. D. Mesecar, J. K. Grimsley, T. Holton, J. R. Wild
Date
:
01 Sep 03 (Deposition) - 30 Nov 04 (Release) - 30 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Organophosphorous Hydrolase, Phosphotriesterase, Vx, Rvx, 4- Methylbenzylphosphonate, Mutant
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. K. Grimsley, B. Calamini, J. R. Wild, A. D. Mesecar
Structural And Mutational Studies Of Organophosphorus Hydrolase Reveal A Cryptic And Functional Allosteric-Binding Site.
Arch. Biochem. Biophys. V. 442 169 2005
(for further references see the
PDB file header
)
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
2a: DIETHYL 4-METHYLBENZYLPHOSPHONATE (EBPa)
2b: DIETHYL 4-METHYLBENZYLPHOSPHONATE (EBPb)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
4
Ligand/Ion
COBALT (II) ION
2
EBP
2
Ligand/Ion
DIETHYL 4-METHYLBENZYLPHOSPHONATE
3
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
NA
2
Ligand/Ion
SODIUM ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
KCX A:169 , HIS A:201 , HIS A:230 , ARG A:254 , CO A:602 , HOH A:802 , HOH A:826
BINDING SITE FOR RESIDUE CO A 601
2
AC2
SOFTWARE
HIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , CO A:601 , HOH A:802
BINDING SITE FOR RESIDUE CO A 602
3
AC3
SOFTWARE
HIS B:55 , HIS B:57 , KCX B:169 , ASP B:301 , CO B:604 , HOH B:774
BINDING SITE FOR RESIDUE CO B 603
4
AC4
SOFTWARE
KCX B:169 , HIS B:201 , HIS B:230 , ARG B:254 , CO B:603 , HOH B:774 , HOH B:776
BINDING SITE FOR RESIDUE CO B 604
5
AC5
SOFTWARE
ASN A:38 , ILE A:154 , HOH A:913 , HOH B:719
BINDING SITE FOR RESIDUE NA A 605
6
AC6
SOFTWARE
ASN B:38 , ILE B:154 , HOH B:802 , HOH B:830
BINDING SITE FOR RESIDUE NA B 606
7
AC7
SOFTWARE
GLN A:155 , TYR A:156 , GLU B:71 , THR B:350
BINDING SITE FOR RESIDUE EBP B 701
8
AC8
SOFTWARE
PHE A:51 , GLU A:71 , HOH A:969 , GLN B:155 , TYR B:156 , ARG B:164
BINDING SITE FOR RESIDUE EBP A 702
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PHOSPHOTRIESTERASE_2 (A:35-363,B:35-363)
2: PHOSPHOTRIESTERASE_1 (A:50-58,B:50-58)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHOTRIESTERASE_2
PS51347
Phosphotriesterase family profile.
OPD_BREDI
35-363
2
A:35-363
B:35-363
2
PHOSPHOTRIESTERASE_1
PS01322
Phosphotriesterase family signature 1.
OPD_BREDI
50-58
2
A:50-58
B:50-58
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1qw7a_ (A:)
1b: SCOP_d1qw7b_ (B:)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Phosphotriesterase-like
(43)
Protein domain
:
Phosphotriesterase (parathion hydrolase, PTE)
(39)
Pseudomonas diminuta [TaxId: 293]
(19)
1a
d1qw7a_
A:
1b
d1qw7b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1qw7A00 (A:30-365)
1b: CATH_1qw7B00 (B:30-365)
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)
Organisms
(
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(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Brevundimonas diminuta. Organism_taxid: 293.
(7)
1a
1qw7A00
A:30-365
1b
1qw7B00
B:30-365
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PTE_1qw7B01 (B:44-359)
1b: PFAM_PTE_1qw7B02 (B:44-359)
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Clan
:
Amidohydrolase
(126)
Family
:
PTE
(19)
Brevundimonas diminuta (Pseudomonas diminuta)
(8)
1a
PTE-1qw7B01
B:44-359
1b
PTE-1qw7B02
B:44-359
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Asymmetric Unit 1
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