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2C0U
Asym. Unit
Info
Asym.Unit (296 KB)
Biol.Unit 1 (286 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A COVALENT COMPLEX OF NITROALKANE OXIDASE TRAPPED DURING SUBSTRATE TURNOVER
Authors
:
A. Nagpal, M. P. Valley, P. F. Fitzpatrick, A. M. Orville
Date
:
07 Sep 05 (Deposition) - 01 Feb 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, N5-Fad Adduct, Flavoenzyme, Nitroalkane, Acyl-Coa Dehydrogenase, Nitrobutyl, Fad, 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
(3, 60)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2as: SELENOMETHIONINE (MSEas)
2at: SELENOMETHIONINE (MSEat)
2au: SELENOMETHIONINE (MSEau)
2av: SELENOMETHIONINE (MSEav)
2aw: SELENOMETHIONINE (MSEaw)
2ax: SELENOMETHIONINE (MSEax)
2ay: SELENOMETHIONINE (MSEay)
2az: SELENOMETHIONINE (MSEaz)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: (2S)-2-NITROBUTANE (NBTa)
3b: (2S)-2-NITROBUTANE (NBTb)
3c: (2S)-2-NITROBUTANE (NBTc)
3d: (2S)-2-NITROBUTANE (NBTd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
MSE
52
Mod. Amino Acid
SELENOMETHIONINE
3
NBT
4
Ligand/Ion
(2S)-2-NITROBUTANE
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:131 , HIS A:133 , SER A:134 , GLY A:138 , THR A:139 , ALA A:140 , ASN A:141 , TRP A:169 , PRO A:170 , SER A:171 , LEU A:400 , PHE A:401 , ASP A:402 , GLY A:403 , GLY A:404 , ILE A:406 , GLY A:407 , ARG A:411 , NBT A:1433 , HOH A:2032 , HOH A:2153 , HOH A:2170 , HOH A:2171 , ARG B:304 , ILE B:310 , HIS B:313 , VAL B:316 , LYS B:375 , ALA B:376 , VAL B:377 , GLY B:378 , MSE B:379 , HOH B:2153 , GLN C:314
BINDING SITE FOR RESIDUE FAD A1432
2
AC2
SOFTWARE
VAL A:95 , ALA A:96 , LEU A:99 , SER A:171 , SER A:276 , PHE A:401 , ASP A:402 , FAD A:1432
BINDING SITE FOR RESIDUE NBT A1433
3
AC3
SOFTWARE
ARG A:304 , ILE A:310 , HIS A:313 , VAL A:316 , LYS A:375 , ALA A:376 , VAL A:377 , GLY A:378 , MSE A:379 , HOH A:2144 , LEU B:99 , LEU B:131 , HIS B:133 , SER B:134 , GLY B:138 , THR B:139 , ALA B:140 , ASN B:141 , TRP B:169 , SER B:171 , LEU B:400 , PHE B:401 , ASP B:402 , GLY B:403 , GLY B:404 , ILE B:406 , GLY B:407 , NBT B:1433 , HOH B:2161 , HOH B:2173 , HOH B:2174 , HOH B:2175 , GLN D:314
BINDING SITE FOR RESIDUE FAD B1432
4
AC4
SOFTWARE
ILE B:92 , VAL B:95 , ALA B:96 , LEU B:99 , SER B:171 , PHE B:401 , ASP B:402 , FAD B:1432
BINDING SITE FOR RESIDUE NBT B1433
5
AC5
SOFTWARE
GLN A:314 , LEU C:131 , HIS C:133 , SER C:134 , GLY C:138 , THR C:139 , ALA C:140 , ASN C:141 , TRP C:169 , SER C:171 , LEU C:400 , PHE C:401 , ASP C:402 , GLY C:403 , GLY C:404 , GLY C:407 , NBT C:1433 , HOH C:2179 , HOH C:2202 , HOH C:2203 , HOH C:2204 , ARG D:304 , ILE D:310 , HIS D:313 , VAL D:316 , LYS D:375 , ALA D:376 , VAL D:377 , GLY D:378 , MSE D:379 , HOH D:2115
BINDING SITE FOR RESIDUE FAD C1432
6
AC6
SOFTWARE
VAL C:95 , ALA C:96 , LEU C:99 , SER C:171 , SER C:276 , PHE C:401 , ASP C:402 , FAD C:1432
BINDING SITE FOR RESIDUE NBT C1433
7
AC7
SOFTWARE
GLN B:314 , ARG C:304 , ILE C:310 , HIS C:313 , VAL C:316 , LYS C:375 , ALA C:376 , VAL C:377 , GLY C:378 , MSE C:379 , LEU D:131 , HIS D:133 , SER D:134 , GLY D:138 , THR D:139 , ALA D:140 , ASN D:141 , TRP D:169 , SER D:171 , LEU D:400 , PHE D:401 , ASP D:402 , GLY D:403 , GLY D:404 , GLY D:407 , ARG D:411 , NBT D:1433 , HOH D:2137 , HOH D:2139 , HOH D:2140 , HOH D:2141 , HOH D:2142
BINDING SITE FOR RESIDUE FAD D1432
8
AC8
SOFTWARE
VAL D:95 , ALA D:96 , LEU D:99 , SER D:171 , PHE D:401 , ASP D:402 , FAD D:1432
BINDING SITE FOR RESIDUE NBT D1433
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2c0ua1 (A:261-430)
1b: SCOP_d2c0ub1 (B:261-431)
1c: SCOP_d2c0uc1 (C:261-431)
1d: SCOP_d2c0ud1 (D:261-431)
2a: SCOP_d2c0ua2 (A:2-260)
2b: SCOP_d2c0ub2 (B:2-260)
2c: SCOP_d2c0uc2 (C:2-260)
2d: SCOP_d2c0ud2 (D:2-260)
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(
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(
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d2c0ua1
A:261-430
1b
d2c0ub1
B:261-431
1c
d2c0uc1
C:261-431
1d
d2c0ud1
D: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
d2c0ua2
A:2-260
2b
d2c0ub2
B:2-260
2c
d2c0uc2
C:2-260
2d
d2c0ud2
D:2-260
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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Chain D
Asymmetric Unit 1
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