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2C13
Biol. Unit 1
Info
Asym.Unit (129 KB)
Biol.Unit 1 (479 KB)
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(1)
Title
:
5-HYDROXY-LEVULINIC ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
Authors
:
F. Frere, M. Nentwich, S. Gacond, D. W. Heinz, R. Neier, N. Frankenberg-Dinkel
Date
:
11 Sep 05 (Deposition) - 20 Jun 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (4x)
Keywords
:
Enzyme Mechanism, Metalloenzyme, Porphobilinogen Synthase, Cocrystallization, Lyase, Porphyrin Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Frere, M. Nentwich, S. Gacond, D. W. Heinz, R. Neier, N. Frankenberg-Dinkel
Probing The Active Site Of Pseudomonas Aeruginosa Porphobilinogen Synthase Using Newly Developed Inhibitors.
Biochemistry V. 45 8243 2006
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Hetero Components
(3, 28)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: (E)-N~6~-[3-CARBOXY-1-(HYDROXYMETH... (FHLa)
2b: (E)-N~6~-[3-CARBOXY-1-(HYDROXYMETH... (FHLb)
2c: (E)-N~6~-[3-CARBOXY-1-(HYDROXYMETH... (FHLc)
2d: (E)-N~6~-[3-CARBOXY-1-(HYDROXYMETH... (FHLd)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
6a: TRIETHYLENE GLYCOL (PGEa)
6b: TRIETHYLENE GLYCOL (PGEb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
FHL
16
Mod. Amino Acid
(E)-N~6~-[3-CARBOXY-1-(HYDROXYMETHYL)PROPYLIDENE]-L-LYSINE
3
K
-1
Ligand/Ion
POTASSIUM ION
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
PEG
4
Ligand/Ion
DI(HYDROXYETHYL)ETHER
6
PGE
8
Ligand/Ion
TRIETHYLENE GLYCOL
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Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:181 , GLU A:245 , HOH A:2144 , HOH A:2181 , HOH A:2182 , HOH A:2183 , HOH A:2185
BINDING SITE FOR RESIDUE MG A1336
2
AC2
SOFTWARE
HIS A:194 , THR A:195 , ASN A:196
BINDING SITE FOR RESIDUE CL A1337
3
AC3
SOFTWARE
ASP A:36 , ASP A:37 , ASP A:319 , HOH A:2222 , ARG B:26 , LEU B:27 , HOH B:2037
BINDING SITE FOR RESIDUE K A1339
4
AC4
SOFTWARE
GLU B:245 , HOH B:2145 , HOH B:2146 , HOH B:2149 , HOH B:2189 , HOH B:2191
BINDING SITE FOR RESIDUE MG B1336
5
AC5
SOFTWARE
THR B:195 , ASN B:196 , HOH B:2156
BINDING SITE FOR RESIDUE CL B1337
6
AC6
SOFTWARE
ARG A:26 , LEU A:27 , HOH A:2039 , HOH A:2040 , ASP B:36 , ASP B:37 , ASP B:319
BINDING SITE FOR RESIDUE K B1340
7
AC7
SOFTWARE
PRO A:55 , ASN B:298 , TRP B:300 , HOH B:2228
BINDING SITE FOR RESIDUE PGE B1338
8
AC8
SOFTWARE
ALA A:207 , ALA A:209 , ASP A:235 , PRO A:236 , ALA A:237 , ARG B:29 , SER B:304 , GLU B:308 , HOH B:2043 , HOH B:2229
BINDING SITE FOR RESIDUE PGE B1339
9
AC9
SOFTWARE
GLY A:183 , GLU A:187 , ALA A:251 , GLU A:252 , HOH A:2227 , TYR B:12
BINDING SITE FOR RESIDUE PEG A1338
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: D_ALA_DEHYDRATASE (A:253-265,B:253-265)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_ALA_DEHYDRATASE
PS00169
Delta-aminolevulinic acid dehydratase active site.
HEM2_PSEAE
253-265
8
A:253-265
B:253-265
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2c13a_ (A:)
1b: SCOP_d2c13b_ (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
:
Aldolase
(457)
Family
:
5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)
(36)
Protein domain
:
automated matches
(15)
Pseudomonas aeruginosa [TaxId: 287]
(8)
1a
d2c13a_
A:
1b
d2c13b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2c13B00 (B:2-336)
1b: CATH_2c13A00 (A:3-336)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Pseudomonas aeruginosa. Organism_taxid: 287.
(10)
1a
2c13B00
B:2-336
1b
2c13A00
A:3-336
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Pfam Domains
(0, 0)
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Asym.Unit (129 KB)
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