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.
1VAO
Asym. Unit
Info
Asym.Unit (193 KB)
Biol.Unit 1 (730 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE
Authors
:
A. Mattevi
Date
:
10 Apr 97 (Deposition) - 15 Oct 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (4x)
Keywords
:
Flavoenzyme, Oxidase, Catalysis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Mattevi, M. W. Fraaije, A. Mozzarelli, L. Olivi, A. Coda, W. J. Van Berkel
Crystal Structures And Inhibitor Binding In The Octameric Flavoenzyme Vanillyl-Alcohol Oxidase: The Shape Of The Active-Site Cavity Controls Substrate Specificity.
Structure V. 5 907 1997
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CL
2
Ligand/Ion
CHLORIDE ION
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: FAD (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:108 , ILE A:468 , TYR A:503 , ARG A:504 , FAD A:600
BINDING SITE FOR RESIDUE ACT A 601
2
AC2
SOFTWARE
TYR B:108 , ILE B:468 , TYR B:503 , ARG B:504 , FAD B:600
BINDING SITE FOR RESIDUE ACT B 601
3
AC3
SOFTWARE
LEU A:171 , FAD A:600
BINDING SITE FOR RESIDUE CL A 602
4
AC4
SOFTWARE
LEU B:171 , FAD B:600
BINDING SITE FOR RESIDUE CL B 602
5
AC5
SOFTWARE
PRO A:99 , ILE A:100 , SER A:101 , ILE A:102 , GLY A:103 , ARG A:104 , ASN A:105 , PRO A:169 , ASP A:170 , GLY A:174 , SER A:175 , ASN A:179 , GLU A:182 , GLY A:184 , VAL A:185 , TYR A:187 , GLY A:260 , VAL A:262 , TRP A:413 , ILE A:414 , HIS A:422 , PHE A:424 , ARG A:504 , LYS A:545 , ACT A:601 , CL A:602 , HOH A:623 , HOH A:637 , HOH A:674 , HOH A:716
BINDING SITE FOR RESIDUE FAD A 600
6
AC6
SOFTWARE
PRO B:99 , ILE B:100 , SER B:101 , ILE B:102 , GLY B:103 , ARG B:104 , ASN B:105 , PRO B:169 , ASP B:170 , GLY B:174 , SER B:175 , ASN B:179 , GLU B:182 , GLY B:184 , VAL B:185 , TYR B:187 , GLY B:260 , VAL B:262 , TRP B:413 , ILE B:414 , HIS B:422 , PHE B:424 , ARG B:504 , LYS B:545 , ACT B:601 , CL B:602 , HOH B:614 , HOH B:679
BINDING SITE FOR RESIDUE FAD B 600
7
FAD
UNKNOWN
FAD A:600 , FAD B:600
COFACTOR.
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: FAD_PCMH (A:67-272,B:67-272)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_PCMH
PS51387
PCMH-type FAD-binding domain profile.
VAOX_PENSI
67-272
2
A:67-272
B:67-272
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1vaoa2 (A:6-273)
1b: SCOP_d1vaob2 (B:6-273)
2a: SCOP_d1vaoa1 (A:274-560)
2b: SCOP_d1vaob1 (B:274-560)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-binding/transporter-associated domain-like
(99)
Superfamily
:
FAD-binding/transporter-associated domain-like
(99)
Family
:
FAD-linked oxidases, N-terminal domain
(29)
Protein domain
:
Vanillyl-alcohol oxidase
(16)
Fungus (Penicillium simplicissimum) [TaxId: 69488]
(16)
1a
d1vaoa2
A:6-273
1b
d1vaob2
B:6-273
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
FAD-linked oxidases, C-terminal domain
(42)
Family
:
Vanillyl-alcohol oxidase-like
(20)
Protein domain
:
Vanillyl-alcohol oxidase
(16)
Fungus (Penicillium simplicissimum) [TaxId: 69488]
(16)
2a
d1vaoa1
A:274-560
2b
d1vaob1
B:274-560
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1vaoA01 (A:6-128)
1b: CATH_1vaoB01 (B:6-128)
2a: CATH_1vaoA02 (A:129-151,A:165-215,A:235-271)
2b: CATH_1vaoB02 (B:129-151,B:165-215,B:235-271)
3a: CATH_1vaoA03 (A:276-506)
3b: CATH_1vaoB03 (B:276-506)
4a: CATH_1vaoA04 (A:507-558)
4b: CATH_1vaoB04 (B:507-558)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
(50)
Homologous Superfamily
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
(50)
Penicillium simplicissimum. Organism_taxid: 69488.
(15)
1a
1vaoA01
A:6-128
1b
1vaoB01
B:6-128
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
(63)
Homologous Superfamily
:
[code=3.30.465.10, no name defined]
(63)
Penicillium simplicissimum. Organism_taxid: 69488.
(15)
2a
1vaoA02
A:129-151,A:165-215,A:235-271
2b
1vaoB02
B:129-151,B:165-215,B:235-271
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Vanillyl-alcohol Oxidase; Chain A, domain 3
(23)
Homologous Superfamily
:
Vanillyl-alcohol Oxidase; Chain A, domain 3
(23)
Penicillium simplicissimum. Organism_taxid: 69488.
(15)
3a
1vaoA03
A:276-506
3b
1vaoB03
B:276-506
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Vanillyl-alcohol Oxidase; Chain A, domain 4
(22)
Homologous Superfamily
:
Vanillyl-alcohol Oxidase; Chain A, domain 4
(22)
Penicillium simplicissimum. Organism_taxid: 69488.
(15)
4a
1vaoA04
A:507-558
4b
1vaoB04
B:507-558
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_FAD_oxidase_C_1vaoB01 (B:306-546)
1b: PFAM_FAD_oxidase_C_1vaoB02 (B:306-546)
2a: PFAM_FAD_binding_4_1vaoB03 (B:71-213)
2b: PFAM_FAD_binding_4_1vaoB04 (B:71-213)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD-oxidase_C
(26)
Family
:
FAD-oxidase_C
(13)
Penicillium simplicissimum
(8)
1a
FAD-oxidase_C-1vaoB01
B:306-546
1b
FAD-oxidase_C-1vaoB02
B:306-546
Clan
:
FAD_PCMH
(53)
Family
:
FAD_binding_4
(31)
Penicillium simplicissimum
(8)
2a
FAD_binding_4-1vaoB03
B:71-213
2b
FAD_binding_4-1vaoB04
B:71-213
[
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 (193 KB)
Header - Asym.Unit
Biol.Unit 1 (730 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
1VAO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
