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2C12
Biol. Unit 2
Info
Asym.Unit (439 KB)
Biol.Unit 1 (289 KB)
Biol.Unit 2 (290 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NITROALKANE OXIDASE IN COMPLEX WITH SPERMINE, A COMPETITIVE INHIBITOR
Authors
:
A. Nagpal, M. P. Valley, P. F. Fitzpatrick, A. M. Orville
Date
:
10 Sep 05 (Deposition) - 01 Feb 06 (Release) - 04 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.07
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F (2x)
Keywords
:
Oxidoreductase, Flavoenzyme, Nitroalkane, Acyl-Coa Dehydrogenase, Long Cell Edge, Fad, Inhibitor, Flavoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Nagpal, M. P. Valley, P. F. Fitzpatrick, A. M. Orville
Crystal Structures Of Nitroalkane Oxidase: Insights Into The Reaction Mechanism From A Covalent Complex Of The Flavoenzyme Trapped During Turnover.
Biochemistry V. 45 1138 2006
(for further references see the
PDB file header
)
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
1e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
1f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
3a: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)... (PE4a)
3b: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)... (PE4b)
4a: SPERMINE (SPMa)
4b: SPERMINE (SPMb)
4c: SPERMINE (SPMc)
4d: SPERMINE (SPMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
GOL
8
Ligand/Ion
GLYCEROL
3
PE4
2
Ligand/Ion
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4
SPM
2
Ligand/Ion
SPERMINE
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Sites
(8, 8)
Info
All Sites
1: AC4 (SOFTWARE)
2: BC1 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
5: CC6 (SOFTWARE)
6: CC7 (SOFTWARE)
7: CC8 (SOFTWARE)
8: CC9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
MET F:70 , LEU F:73 , GLU F:76 , VAL F:95 , MET F:102 , SER F:276 , PHE F:401 , ASP F:402 , FAD F:1432 , HOH F:2199
BINDING SITE FOR RESIDUE SPM F1433
2
BC1
SOFTWARE
LEU E:131 , HIS E:133 , SER E:134 , GLY E:138 , THR E:139 , ALA E:140 , ASN E:141 , TRP E:169 , PRO E:170 , SER E:171 , THR E:240 , GLN E:314 , LEU E:400 , PHE E:401 , ASP E:402 , GLY E:403 , GLY E:404 , ILE E:406 , GLY E:407 , ARG E:411 , HOH E:2178 , HOH E:2179 , HOH E:2180 , HOH E:2181 , HOH E:2182 , HOH E:2183 , HOH E:2184 , ARG F:304 , ILE F:310 , HIS F:313 , VAL F:316 , LYS F:375 , ALA F:376 , VAL F:377 , GLY F:378 , MET F:379
BINDING SITE FOR RESIDUE FAD E1432
3
BC2
SOFTWARE
ARG E:304 , ILE E:310 , HIS E:313 , VAL E:316 , LYS E:375 , ALA E:376 , VAL E:377 , GLY E:378 , MET E:379 , HOH E:2154 , LEU F:131 , HIS F:133 , SER F:134 , GLY F:138 , THR F:139 , ALA F:140 , ASN F:141 , TRP F:169 , PRO F:170 , SER F:171 , GLN F:314 , LEU F:400 , PHE F:401 , ASP F:402 , GLY F:403 , GLY F:404 , ILE F:406 , GLY F:407 , LEU F:408 , ARG F:411 , SPM F:1433 , HOH F:2195 , HOH F:2196 , HOH F:2197 , HOH F:2198
BINDING SITE FOR RESIDUE FAD F1432
4
BC3
SOFTWARE
LEU F:341 , GLU F:342 , LYS F:351 , HOH F:2203 , HOH F:2204 , HOH F:2205
BINDING SITE FOR RESIDUE PE4 F1435
5
CC6
SOFTWARE
ASP E:322 , ILE E:360 , ASP E:364 , ARG E:410
BINDING SITE FOR RESIDUE GOL E1433
6
CC7
SOFTWARE
GLU E:368 , ILE E:371 , ASP E:372 , LYS E:375 , GOL E:1435 , HOH E:2185 , HOH E:2186 , GLU F:368 , HOH F:2164
BINDING SITE FOR RESIDUE GOL E1434
7
CC8
SOFTWARE
LYS E:319 , ARG E:326 , ASP E:372 , LYS E:375 , GOL E:1434 , HOH E:2151 , HOH E:2186 , HOH E:2187 , HOH F:2200
BINDING SITE FOR RESIDUE GOL E1435
8
CC9
SOFTWARE
ASP F:322 , ILE F:325 , TYR F:361 , ASP F:364 , ARG F:410 , HOH F:2147 , HOH F:2200 , HOH F:2201 , HOH F:2202
BINDING SITE FOR RESIDUE GOL F1434
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2c12a1 (A:261-431)
1b: SCOP_d2c12b1 (B:261-431)
1c: SCOP_d2c12c1 (C:261-431)
1d: SCOP_d2c12d1 (D:261-431)
1e: SCOP_d2c12e1 (E:261-431)
1f: SCOP_d2c12f1 (F:261-431)
2a: SCOP_d2c12a2 (A:2-260)
2b: SCOP_d2c12b2 (B:2-260)
2c: SCOP_d2c12c2 (C:2-260)
2d: SCOP_d2c12d2 (D:2-260)
2e: SCOP_d2c12e2 (E:2-260)
2f: SCOP_d2c12f2 (F:2-260)
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Protein Domains
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Organisms
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)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
Nitroalkane oxidase
(2)
Fungus (Fusarium oxysporum) [TaxId: 5507]
(2)
1a
d2c12a1
A:261-431
1b
d2c12b1
B:261-431
1c
d2c12c1
C:261-431
1d
d2c12d1
D:261-431
1e
d2c12e1
E:261-431
1f
d2c12f1
F:261-431
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
(32)
Protein domain
:
Nitroalkane oxidase
(2)
Fungus (Fusarium oxysporum) [TaxId: 5507]
(2)
2a
d2c12a2
A:2-260
2b
d2c12b2
B:2-260
2c
d2c12c2
C:2-260
2d
d2c12d2
D:2-260
2e
d2c12e2
E:2-260
2f
d2c12f2
F:2-260
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CATH Domains
(0, 0)
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Pfam Domains
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Asym.Unit (439 KB)
Header - Asym.Unit
Biol.Unit 1 (289 KB)
Header - Biol.Unit 1
Biol.Unit 2 (290 KB)
Header - Biol.Unit 2
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