PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2C12
Asym. Unit
Info
Asym.Unit (439 KB)
Biol.Unit 1 (289 KB)
Biol.Unit 2 (290 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
)
[
close entry info
]
Hetero Components
(4, 27)
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
6
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
GOL
15
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
4
Ligand/Ion
SPERMINE
[
close Hetero Component info
]
Sites
(27, 27)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET B:70 , GLU B:76 , VAL B:95 , ALA B:98 , SER B:276 , LEU B:279 , PHE B:401 , ASP B:402 , FAD B:1432 , HOH B:2201
BINDING SITE FOR RESIDUE SPM B1433
02
AC2
SOFTWARE
MET C:70 , LEU C:73 , GLU C:76 , VAL C:95 , LEU C:99 , MET C:102 , PHE C:273 , SER C:276 , LEU C:279 , ASP C:402 , FAD C:1433 , HOH C:2164
BINDING SITE FOR RESIDUE SPM C1434
03
AC3
SOFTWARE
MET D:70 , GLU D:76 , VAL D:95 , ALA D:98 , MET D:102 , SER D:276 , LEU D:279 , PHE D:401 , ASP D:402 , FAD D:1433
BINDING SITE FOR RESIDUE SPM D1434
04
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
05
AC5
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 , HOH A:2078 , HOH A:2179 , HOH A:2190 , HOH A:2191 , HOH A:2192 , HOH A:2194 , HOH A:2195 , ARG B:304 , ILE B:310 , HIS B:313 , VAL B:316 , LYS B:375 , ALA B:376 , VAL B:377 , GLY B:378 , MET B:379 , HOH B:2166 , HOH B:2167 , GLN C:314
BINDING SITE FOR RESIDUE FAD A1432
06
AC6
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 , MET A:379 , LEU B:131 , HIS B:133 , SER B:134 , GLY B:138 , THR B:139 , ALA B:140 , ASN B:141 , TRP B:169 , PRO B:170 , SER B:171 , LEU B:400 , PHE B:401 , ASP B:402 , GLY B:403 , GLY B:404 , ILE B:406 , GLY B:407 , LEU B:408 , ARG B:411 , SPM B:1433 , HOH B:2079 , HOH B:2195 , HOH B:2196 , HOH B:2197 , HOH B:2198 , HOH B:2199 , HOH B:2200 , GLN D:314
BINDING SITE FOR RESIDUE FAD B1432
07
AC7
SOFTWARE
LEU B:341 , GLU B:342 , LYS B:351 , HOH B:2204 , HOH B:2206 , HOH B:2207
BINDING SITE FOR RESIDUE PE4 B1436
08
AC8
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 , PRO C:170 , SER C:171 , LEU C:400 , PHE C:401 , ASP C:402 , GLY C:403 , GLY C:404 , ILE C:406 , GLY C:407 , ARG C:411 , SPM C:1434 , HOH C:2065 , HOH C:2160 , HOH C:2161 , HOH C:2162 , HOH C:2163 , ARG D:304 , ILE D:310 , HIS D:313 , VAL D:316 , LYS D:375 , ALA D:376 , VAL D:377 , GLY D:378 , MET D:379 , HOH D:2130
BINDING SITE FOR RESIDUE FAD C1433
09
AC9
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 , MET C:379 , HOH C:2131 , LEU D:131 , HIS D:133 , SER D:134 , GLY D:138 , THR D:139 , ALA D:140 , ASN D:141 , TRP D:169 , PRO D:170 , SER D:171 , LEU D:400 , PHE D:401 , ASP D:402 , GLY D:403 , GLY D:404 , ILE D:406 , GLY D:407 , LEU D:408 , SPM D:1434 , HOH D:2154 , HOH D:2155 , HOH D:2156 , HOH D:2157 , HOH D:2158
BINDING SITE FOR RESIDUE FAD D1433
10
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
11
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
12
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
13
BC4
SOFTWARE
GLU A:71 , GLU A:342 , HOH A:2030
BINDING SITE FOR RESIDUE GOL A1433
14
BC5
SOFTWARE
ILE B:360 , ASP B:364 , ARG B:410 , GOL B:1435 , HOH B:2163 , HOH B:2202 , HOH B:2203 , ASP D:322
BINDING SITE FOR RESIDUE GOL B1434
15
BC6
SOFTWARE
LYS A:375 , ASP B:364 , GLU B:368 , GOL B:1434 , HOH B:2162 , HOH B:2163 , HOH B:2202 , HOH B:2203
BINDING SITE FOR RESIDUE GOL B1435
16
BC7
SOFTWARE
ILE A:360 , ASP A:364 , ASP C:322 , ARG C:326
BINDING SITE FOR RESIDUE GOL C1432
17
BC8
SOFTWARE
ASP A:322 , ILE A:325 , ILE C:360 , ASP C:364 , ARG C:410
BINDING SITE FOR RESIDUE GOL C1435
18
BC9
SOFTWARE
VAL A:2 , GLN C:10 , SER C:72 , VAL C:74 , GLU C:342
BINDING SITE FOR RESIDUE GOL C1436
19
CC1
SOFTWARE
ILE C:371 , ASP C:372 , LYS C:375 , HOH C:2127 , HOH C:2132 , ASP D:364 , VAL D:367 , GLU D:368 , GOL D:1432
BINDING SITE FOR RESIDUE GOL C1437
20
CC2
SOFTWARE
GLU C:368 , GOL C:1437 , HOH C:2125 , ASP D:372 , LYS D:375 , HOH D:2127 , HOH D:2153
BINDING SITE FOR RESIDUE GOL D1432
21
CC3
SOFTWARE
THR D:26 , SER D:29 , VAL D:86 , HOH D:2159
BINDING SITE FOR RESIDUE GOL D1435
22
CC4
SOFTWARE
ASP B:322 , ILE D:360 , ASP D:364 , ARG D:410
BINDING SITE FOR RESIDUE GOL D1436
23
CC5
SOFTWARE
ALA D:13 , HIS D:16 , ALA D:17 , ILE D:79 , HOH D:2024
BINDING SITE FOR RESIDUE GOL D1437
24
CC6
SOFTWARE
ASP E:322 , ILE E:360 , ASP E:364 , ARG E:410
BINDING SITE FOR RESIDUE GOL E1433
25
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
26
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
27
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
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
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
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
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
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2C12
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help