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.
2GV8
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (154 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 FLAVIN-CONTAINING MONOOXYGENASE (FMO) FROM S.POMBE AND NADPH COFACTOR COMPLEX
Authors
:
S. Eswaramoorthy, S. Swaminathan, S. K. Burley, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date
:
02 May 06 (Deposition) - 06 Jun 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Fmo, Fad, Nadph, Cofactor Complex, Oxygenase, Psi, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Eswaramoorthy, J. B. Bonanno, S. K. Burley, S. Swaminathan
Mechanism Of Action Of A Flavin-Containing Monooxygenase.
Proc. Natl. Acad. Sci. Usa V. 103 9832 2006
[
close entry info
]
Hetero Components
(4, 14)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
4a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
4b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
GOL
2
Ligand/Ion
GLYCEROL
3
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
4
NDP
2
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:13 , GLY A:15 , PRO A:16 , SER A:17 , GLU A:38 , ARG A:39 , ARG A:40 , GLY A:45 , VAL A:46 , TRP A:47 , PRO A:83 , LEU A:84 , LEU A:88 , THR A:90 , ASN A:91 , THR A:92 , THR A:136 , ASP A:137 , VAL A:138 , CYS A:172 , ASN A:173 , GLY A:174 , TYR A:176 , PHE A:296 , PRO A:342 , PHE A:343 , NDP A:501 , HOH A:503 , HOH A:508 , HOH A:511 , HOH A:512 , HOH A:527 , HOH A:542 , HOH A:545 , HOH A:599 , HOH A:627 , HOH A:673
BINDING SITE FOR RESIDUE FAD A 500
2
AC2
SOFTWARE
GLY B:13 , GLY B:15 , PRO B:16 , SER B:17 , GLU B:38 , ARG B:39 , ARG B:40 , GLY B:45 , VAL B:46 , TRP B:47 , PRO B:83 , LEU B:84 , LEU B:88 , THR B:90 , ASN B:91 , THR B:92 , THR B:136 , ASP B:137 , VAL B:138 , CYS B:172 , ASN B:173 , GLY B:174 , TYR B:176 , PHE B:296 , PRO B:342 , PHE B:343 , NDP B:501 , HOH B:503 , HOH B:508 , HOH B:511 , HOH B:529 , HOH B:531 , HOH B:532 , HOH B:539 , HOH B:562 , HOH B:570 , HOH B:622 , HOH B:626
BINDING SITE FOR RESIDUE FAD B 500
3
AC3
SOFTWARE
TYR A:85 , GLN A:89 , ASN A:91 , TYR A:176 , GLY A:219 , ALA A:221 , SER A:222 , SER A:223 , ASP A:226 , SER A:242 , LEU A:244 , CYS A:287 , THR A:288 , FAD A:500 , HOH A:533 , HOH A:535 , HOH A:563 , HOH A:570 , HOH A:579 , HOH A:602 , HOH A:648 , HOH A:661 , HOH A:670 , HOH A:712
BINDING SITE FOR RESIDUE NDP A 501
4
AC4
SOFTWARE
TYR B:85 , GLN B:89 , ASN B:91 , TYR B:176 , GLY B:219 , ALA B:221 , SER B:222 , SER B:223 , ASP B:226 , SER B:242 , LEU B:244 , CYS B:287 , THR B:288 , GLY B:289 , FAD B:500 , HOH B:573 , HOH B:576 , HOH B:594 , HOH B:648 , HOH B:672
BINDING SITE FOR RESIDUE NDP B 501
5
AC5
SOFTWARE
TYR A:49 , SER A:51 , ARG A:86 , GLU A:206 , HOH A:509 , HOH A:653 , HOH A:654 , ASN B:48 , HOH B:636 , HOH B:641
BINDING SITE FOR RESIDUE GOL A 502
6
AC6
SOFTWARE
ASN A:48 , HOH A:585 , TYR B:49 , SER B:51 , ARG B:86 , GLU B:206 , HOH B:505 , HOH B:631 , HOH B:632 , HOH B:702
BINDING SITE FOR RESIDUE GOL B 502
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2gv8a1 (A:3-180,A:288-444)
1b: SCOP_d2gv8a2 (A:181-287)
1c: SCOP_d2gv8b1 (B:3-180,B:288-444)
1d: SCOP_d2gv8b2 (B:181-287)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD/NAD-linked reductases, N-terminal and central domains
(92)
Protein domain
:
Flavin-dependent monoxygenase SPBP16F5.08c
(3)
Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]
(3)
1a
d2gv8a1
A:3-180,A:288-444
1b
d2gv8a2
A:181-287
1c
d2gv8b1
B:3-180,B:288-444
1d
d2gv8b2
B:181-287
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2gv8A02 (A:183-287)
1b: CATH_2gv8B02 (B:183-287)
1c: CATH_2gv8A01 (A:3-182,A:288-444)
1d: CATH_2gv8B01 (B:3-182,B:288-444)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Fission yeast (Schizosaccharomyces pombe)
(3)
1a
2gv8A02
A:183-287
1b
2gv8B02
B:183-287
1c
2gv8A01
A:3-182,A:288-444
1d
2gv8B01
B:3-182,B:288-444
[
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
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 (160 KB)
Header - Asym.Unit
Biol.Unit 1 (154 KB)
Header - Biol.Unit 1
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
2GV8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
