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1W5P
Biol. Unit 1
Info
Asym.Unit (129 KB)
Biol.Unit 1 (476 KB)
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(1)
Title
:
STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS A129C, D131C, D139C, P132E)
Authors
:
F. Frere, H. Reents, W. -D. Schubert, D. W. Heinz, D. Jahn
Date
:
09 Aug 04 (Deposition) - 19 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (4x)
Keywords
:
Synthase, Evolution, Metalloenzyme, Porphobilinogen Synthase, Pseudomonas Aeruginosa, Protein Engineering,
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Frere, H. Reents, W. -D. Schubert, D. W. Heinz, D. Jahn
Tracking The Evolution Of Porphobilinogen Synthase Metal Dependence In Vitro
J. Mol. Biol. V. 345 1059 2005
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Hetero Components
(4, 60)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
2a: FORMIC ACID (FMTa)
2b: FORMIC ACID (FMTb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
4a: POTASSIUM ION (Ka)
4b: POTASSIUM ION (Kb)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
20
Ligand/Ion
1,2-ETHANEDIOL
2
FMT
8
Ligand/Ion
FORMIC ACID
3
GOL
24
Ligand/Ion
GLYCEROL
4
K
-1
Ligand/Ion
POTASSIUM ION
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
SO4
8
Ligand/Ion
SULFATE ION
7
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(21, 21)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:26 , LEU A:27 , ASP B:36 , ASP B:37 , ASP B:319 , GOL B:1345
BINDING SITE FOR RESIDUE K A1341
02
AC2
SOFTWARE
GLU A:245 , HOH A:2171 , HOH A:2173 , HOH A:2210 , HOH A:2211 , HOH A:2212
BINDING SITE FOR RESIDUE MG A1342
03
AC3
SOFTWARE
ARG A:20 , ASN B:196
BINDING SITE FOR RESIDUE SO4 A1343
04
AC4
SOFTWARE
CYS A:129 , CYS A:131 , CYS A:139 , HOH A:2266
BINDING SITE FOR RESIDUE ZN A1345
05
AC5
SOFTWARE
ASP A:36 , ASP A:37 , ASP A:319 , ARG B:26 , LEU B:27 , GOL B:1343 , HOH B:2031
BINDING SITE FOR RESIDUE K B1340
06
AC6
SOFTWARE
GLU B:245 , HOH B:2179 , HOH B:2181 , HOH B:2212 , HOH B:2213 , HOH B:2214
BINDING SITE FOR RESIDUE MG B1341
07
AC7
SOFTWARE
ASN A:196 , ARG B:20 , HOH B:2259
BINDING SITE FOR RESIDUE SO4 B1342
08
AC8
SOFTWARE
CYS B:129 , CYS B:131 , CYS B:139 , HOH B:2265
BINDING SITE FOR RESIDUE ZN B1348
09
AC9
SOFTWARE
ILE A:80 , PRO A:81 , GLU A:121 , HOH A:2262 , ASP B:22 , PHE B:23 , ARG B:26
BINDING SITE FOR RESIDUE EDO A1337
10
BC1
SOFTWARE
ASP A:235 , PRO A:236 , ALA A:237 , ARG B:29 , HOH B:2035
BINDING SITE FOR RESIDUE EDO A1338
11
BC2
SOFTWARE
ARG A:271 , ASP A:274 , HOH A:2224 , ARG B:271 , ASP B:274 , HOH B:2227
BINDING SITE FOR RESIDUE EDO A1339
12
BC3
SOFTWARE
ASP A:22 , PHE A:23 , ARG A:26 , ILE B:80 , GLU B:121 , HOH B:2258
BINDING SITE FOR RESIDUE EDO B1337
13
BC4
SOFTWARE
ASP B:46 , ARG B:110
BINDING SITE FOR RESIDUE EDO B1338
14
BC5
SOFTWARE
TYR A:211 , PHE A:214 , TYR A:283 , VAL A:285 , SER A:286 , TYR A:324
BINDING SITE FOR RESIDUE FMT A1340
15
BC6
SOFTWARE
LEU A:40 , PRO A:41 , VAL A:42 , VAL A:60 , GLU A:61 , HOH A:2069 , HOH A:2070 , HOH A:2255 , HOH A:2264 , HOH A:2265
BINDING SITE FOR RESIDUE GOL A1344
16
BC7
SOFTWARE
TYR B:211 , PHE B:214 , VAL B:285 , SER B:286 , TYR B:324
BINDING SITE FOR RESIDUE FMT B1339
17
BC8
SOFTWARE
THR A:34 , ASP A:37 , LYS A:314 , HOH A:2046 , ARG B:29 , GLU B:30 , ASN B:31 , VAL B:32 , K B:1340 , HOH B:2261
BINDING SITE FOR RESIDUE GOL B1343
18
BC9
SOFTWARE
PRO B:41 , VAL B:42 , VAL B:60 , GLU B:61 , HOH B:2076 , HOH B:2077 , HOH B:2252 , HOH B:2262 , HOH B:2263
BINDING SITE FOR RESIDUE GOL B1344
19
CC1
SOFTWARE
ARG A:29 , GLU A:30 , ASN A:31 , K A:1341 , THR B:34 , ASP B:37 , LYS B:314
BINDING SITE FOR RESIDUE GOL B1345
20
CC2
SOFTWARE
ARG A:29 , ASP B:235 , PRO B:236 , HOH B:2264
BINDING SITE FOR RESIDUE GOL B1346
21
CC3
SOFTWARE
GLN B:138 , ASN B:228 , LYS B:229
BINDING SITE FOR RESIDUE GOL B1347
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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)
;
View:
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End label:
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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Note:
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_d1w5pa_ (A:)
1b: SCOP_d1w5pb_ (B:)
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Protein Domains
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Organisms
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)
(
)
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: 208964]
(6)
1a
d1w5pa_
A:
1b
d1w5pb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1w5pA00 (A:6-336)
1b: CATH_1w5pB00 (B:6-336)
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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: 208964. Strain: pao1.
(6)
1a
1w5pA00
A:6-336
1b
1w5pB00
B:6-336
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_ALAD_1w5pB01 (B:10-333)
1b: PFAM_ALAD_1w5pB02 (B:10-333)
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Clan
:
TIM_barrel
(694)
Family
:
ALAD
(17)
Pseudomonas aeruginosa
(7)
1a
ALAD-1w5pB01
B:10-333
1b
ALAD-1w5pB02
B:10-333
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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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