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2IVD
Biol. Unit 2
Info
Asym.Unit (152 KB)
Biol.Unit 1 (74 KB)
Biol.Unit 2 (75 KB)
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(1)
Title
:
STRUCTURE OF PROTOPORPHYRINOGEN OXIDASE FROM MYXOCOCCUS XANTHUS WITH ACIFLUORFEN
Authors
:
H. R. Corradi, A. V. Corrigall, E. Boix, C. G. Mohan, E. D. Sturrock, P. N. Meissner, K. R. Acharya
Date
:
12 Jun 06 (Deposition) - 17 Oct 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protoporphyrinogen Oxidase, Porphyrin Biosynthesis, Chlorophyll Biosynthesis, Oxidoreductase, Haem Biosynthesis, Heme Biosynthesis, Fad, Porphyria, Acifluorfen, Flavoprotein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
H. R. Corradi, A. V. Corrigall, E. Boix, C. G. Mohan, E. D. Sturrock, P. N. Meissner, K. R. Acharya
Crystal Structure Of Protoporphyrinogen Oxidase From Myxococcus Xanthus And Its Complex With The Inhibitor Acifluorfen.
J. Biol. Chem. V. 281 38625 2006
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Hetero Components
(4, 6)
Info
All Hetero Components
1a: 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHE... (ACJa)
1b: 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHE... (ACJb)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
4a: (3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTET... (TWNa)
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No.
Name
Count
Type
Full Name
1
ACJ
1
Ligand/Ion
5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID
2
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
GOL
3
Ligand/Ion
GLYCEROL
4
TWN
1
Ligand/Ion
(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE
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Sites
(6, 6)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC8 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
ARG B:95 , THR B:166 , GLY B:167 , ILE B:168 , TYR B:169 , ALA B:170 , ILE B:311 , PHE B:329 , GLY B:330 , PHE B:331 , LEU B:332 , ALA B:344 , ILE B:345 , MET B:365 , ILE B:412 , FAD B:1469 , HOH B:2132
BINDING SITE FOR RESIDUE ACJ B1468
2
AC4
SOFTWARE
VAL B:15 , GLY B:16 , GLY B:18 , ILE B:19 , SER B:20 , LEU B:38 , GLU B:39 , SER B:40 , GLY B:46 , ALA B:47 , GLY B:61 , PRO B:62 , ASN B:63 , SER B:64 , VAL B:251 , ALA B:283 , PRO B:284 , ALA B:287 , VAL B:313 , GLY B:440 , ASN B:441 , VAL B:446 , GLY B:447 , LEU B:448 , ACJ B:1468 , HOH B:2001 , HOH B:2129 , HOH B:2133 , HOH B:2134 , HOH B:2136 , HOH B:2137
BINDING SITE FOR RESIDUE FAD B1469
3
AC5
SOFTWARE
LEU B:125 , ARG B:126 , GLY B:129 , ARG B:134 , GOL B:1467 , HOH B:2131 , HOH B:2142
BINDING SITE FOR RESIDUE TWN B1472
4
AC8
SOFTWARE
ARG B:126 , ARG B:193 , TWN B:1472 , HOH B:2045 , HOH B:2131
BINDING SITE FOR RESIDUE GOL B1467
5
AC9
SOFTWARE
PRO B:120 , LEU B:121 , GLY B:122 , ALA B:123 , ARG B:201 , HOH B:2138
BINDING SITE FOR RESIDUE GOL B1470
6
BC1
SOFTWARE
GLY B:122 , ALA B:123 , ARG B:193 , LEU B:197 , ARG B:201 , HOH B:2072 , HOH B:2140 , HOH B:2141
BINDING SITE FOR RESIDUE GOL B1471
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2ivda2 (A:307-414)
1b: SCOP_d2ivdb2 (B:307-414)
2a: SCOP_d2ivda1 (A:10-306,A:415-464)
2b: SCOP_d2ivdb1 (B:10-306,B:415-466)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-linked reductases, C-terminal domain
(181)
Superfamily
:
FAD-linked reductases, C-terminal domain
(181)
Family
:
L-aminoacid/polyamine oxidase
(66)
Protein domain
:
Protoporphyrinogen oxidase
(3)
Myxococcus xanthus [TaxId: 34]
(2)
1a
d2ivda2
A:307-414
1b
d2ivdb2
B:307-414
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD-linked reductases, N-terminal domain
(156)
Protein domain
:
Protoporphyrinogen oxidase
(3)
Myxococcus xanthus [TaxId: 34]
(2)
2a
d2ivda1
A:10-306,A:415-464
2b
d2ivdb1
B:10-306,B:415-466
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CATH Domains
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Pfam Domains
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Chain B
Asymmetric Unit 1
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Asym.Unit (152 KB)
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