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.
1OJD
Biol. Unit 1
Info
Asym.Unit (814 KB)
Biol.Unit 1 (170 KB)
Biol.Unit 2 (171 KB)
Biol.Unit 3 (171 KB)
Biol.Unit 4 (171 KB)
Biol.Unit 5 (170 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN MONOAMINE OXIDASE B IN COMPLEX WITH LAURYLDIMETHYLAMINE-N-OXIDE (LDAO)
Authors
:
C. Binda, D. E. Edmondson, A. Mattevi
Date
:
08 Jul 03 (Deposition) - 15 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,L (1x)
Keywords
:
Oxidoreductase, Fad-Containing Amine Oxidase, Maob
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Binda, M. Li, F. Hubalek, N. Restelli, D. E. Edmondson, A. Mattevi
Insights Into The Mode Of Inhibition Of Human Mitochondrial Monoamine Oxidase B From High-Resolution Crystal Structures
Proc. Natl. Acad. Sci. Usa V. 100 9750 2003
[
close entry info
]
Hetero Components
(2, 4)
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)
1g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
1h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
1i: FLAVIN-ADENINE DINUCLEOTIDE (FADi)
1j: FLAVIN-ADENINE DINUCLEOTIDE (FADj)
2a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
2b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
2c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
2d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
2e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
2f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
2g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
2h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
2i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
2j: LAURYL DIMETHYLAMINE-N-OXIDE (LDAj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
LDA
2
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:11 , GLY A:12 , GLY A:13 , ILE A:14 , SER A:15 , GLU A:34 , ALA A:35 , ARG A:36 , GLY A:40 , GLY A:41 , ARG A:42 , GLY A:58 , SER A:59 , TYR A:60 , PRO A:234 , VAL A:235 , ALA A:263 , ILE A:264 , TRP A:388 , TYR A:393 , CYS A:397 , TYR A:398 , GLY A:425 , THR A:426 , GLY A:434 , TYR A:435 , MET A:436 , ALA A:439 , LDA A:601
BINDING SITE FOR RESIDUE FAD A 600
2
AC2
SOFTWARE
TRP A:119 , LEU A:171 , ILE A:199 , GLN A:206 , PHE A:343 , TYR A:398 , FAD A:600
BINDING SITE FOR RESIDUE LDA A 601
3
AC3
SOFTWARE
GLY B:11 , GLY B:12 , GLY B:13 , ILE B:14 , SER B:15 , LEU B:33 , GLU B:34 , ALA B:35 , ARG B:36 , GLY B:40 , GLY B:41 , ARG B:42 , GLY B:58 , SER B:59 , TYR B:60 , PRO B:234 , VAL B:235 , ALA B:263 , ILE B:264 , TRP B:388 , TYR B:393 , CYS B:397 , TYR B:398 , GLY B:425 , THR B:426 , GLY B:434 , TYR B:435 , MET B:436 , LDA B:601
BINDING SITE FOR RESIDUE FAD B 600
4
AC4
SOFTWARE
TRP B:119 , LEU B:171 , ILE B:199 , GLN B:206 , PHE B:343 , TYR B:398 , FAD B:600
BINDING SITE FOR RESIDUE LDA B 601
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 20)
Info
All SCOP Domains
1a: SCOP_d1ojda2 (A:290-401)
1b: SCOP_d1ojdb2 (B:290-401)
1c: SCOP_d1ojdc2 (C:290-401)
1d: SCOP_d1ojdd2 (D:290-401)
1e: SCOP_d1ojde2 (E:290-401)
1f: SCOP_d1ojdf2 (F:290-401)
1g: SCOP_d1ojdg2 (G:290-401)
1h: SCOP_d1ojdh2 (H:290-401)
1i: SCOP_d1ojdi2 (I:290-401)
1j: SCOP_d1ojdl2 (L:290-401)
2a: SCOP_d1ojda1 (A:4-289,A:402-500)
2b: SCOP_d1ojdb1 (B:4-289,B:402-497)
2c: SCOP_d1ojdc1 (C:4-289,C:402-501)
2d: SCOP_d1ojdd1 (D:4-289,D:402-497)
2e: SCOP_d1ojde1 (E:4-289,E:402-501)
2f: SCOP_d1ojdf1 (F:4-289,F:402-500)
2g: SCOP_d1ojdg1 (G:4-289,G:402-497)
2h: SCOP_d1ojdh1 (H:4-289,H:402-501)
2i: SCOP_d1ojdi1 (I:4-289,I:402-500)
2j: SCOP_d1ojdl1 (L:4-289,L:402-500)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-linked reductases, C-terminal domain
(181)
Superfamily
:
FAD-linked reductases, C-terminal domain
(181)
Family
:
L-aminoacid/polyamine oxidase
(66)
Protein domain
:
Monoamine oxidase B
(38)
Human (Homo sapiens) [TaxId: 9606]
(37)
1a
d1ojda2
A:290-401
1b
d1ojdb2
B:290-401
1c
d1ojdc2
C:290-401
1d
d1ojdd2
D:290-401
1e
d1ojde2
E:290-401
1f
d1ojdf2
F:290-401
1g
d1ojdg2
G:290-401
1h
d1ojdh2
H:290-401
1i
d1ojdi2
I:290-401
1j
d1ojdl2
L:290-401
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD-linked reductases, N-terminal domain
(156)
Protein domain
:
Monoamine oxidase B
(38)
Human (Homo sapiens) [TaxId: 9606]
(37)
2a
d1ojda1
A:4-289,A:402-500
2b
d1ojdb1
B:4-289,B:402-497
2c
d1ojdc1
C:4-289,C:402-501
2d
d1ojdd1
D:4-289,D:402-497
2e
d1ojde1
E:4-289,E:402-501
2f
d1ojdf1
F:4-289,F:402-500
2g
d1ojdg1
G:4-289,G:402-497
2h
d1ojdh1
H:4-289,H:402-501
2i
d1ojdi1
I:4-289,I:402-500
2j
d1ojdl1
L:4-289,L:402-500
[
close SCOP info
]
CATH Domains
(3, 30)
Info
all CATH domains
1a: CATH_1ojdA01 (A:4-41,A:63-78,A:211-289,A:403-463)
1b: CATH_1ojdB01 (B:4-41,B:63-78,B:211-289,B:403-463)
1c: CATH_1ojdC01 (C:4-41,C:63-78,C:211-289,C:403-463)
1d: CATH_1ojdD01 (D:4-41,D:63-78,D:211-289,D:403-463)
1e: CATH_1ojdE01 (E:4-41,E:63-78,E:211-289,E:403-463)
1f: CATH_1ojdF01 (F:4-41,F:63-78,F:211-289,F:403-463)
1g: CATH_1ojdG01 (G:4-41,G:63-78,G:211-289,G:403-463)
1h: CATH_1ojdH01 (H:4-41,H:63-78,H:211-289,H:403-463)
1i: CATH_1ojdI01 (I:4-41,I:63-78,I:211-289,I:403-463)
1j: CATH_1ojdL01 (L:4-41,L:63-78,L:211-289,L:403-463)
2a: CATH_1ojdA02 (A:42-62,A:79-107,A:200-210,A:290-402)
2b: CATH_1ojdB02 (B:42-62,B:79-107,B:200-210,B:290-402)
2c: CATH_1ojdC02 (C:42-62,C:79-107,C:200-210,C:290-402)
2d: CATH_1ojdD02 (D:42-62,D:79-107,D:200-210,D:290-402)
2e: CATH_1ojdE02 (E:42-62,E:79-107,E:200-210,E:290-402)
2f: CATH_1ojdF02 (F:42-62,F:79-107,F:200-210,F:290-402)
2g: CATH_1ojdG02 (G:42-62,G:79-107,G:200-210,G:290-402)
2h: CATH_1ojdH02 (H:42-62,H:79-107,H:200-210,H:290-402)
2i: CATH_1ojdI02 (I:42-62,I:79-107,I:200-210,I:290-402)
2j: CATH_1ojdL02 (L:42-62,L:79-107,L:200-210,L:290-402)
3a: CATH_1ojdA03 (A:108-199)
3b: CATH_1ojdB03 (B:108-199)
3c: CATH_1ojdC03 (C:108-199)
3d: CATH_1ojdD03 (D:108-199)
3e: CATH_1ojdE03 (E:108-199)
3f: CATH_1ojdF03 (F:108-199)
3g: CATH_1ojdG03 (G:108-199)
3h: CATH_1ojdH03 (H:108-199)
3i: CATH_1ojdI03 (I:108-199)
3j: CATH_1ojdL03 (L:108-199)
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)
Human (Homo sapiens)
(57)
1a
1ojdA01
A:4-41,A:63-78,A:211-289,A:403-463
1b
1ojdB01
B:4-41,B:63-78,B:211-289,B:403-463
1c
1ojdC01
C:4-41,C:63-78,C:211-289,C:403-463
1d
1ojdD01
D:4-41,D:63-78,D:211-289,D:403-463
1e
1ojdE01
E:4-41,E:63-78,E:211-289,E:403-463
1f
1ojdF01
F:4-41,F:63-78,F:211-289,F:403-463
1g
1ojdG01
G:4-41,G:63-78,G:211-289,G:403-463
1h
1ojdH01
H:4-41,H:63-78,H:211-289,H:403-463
1i
1ojdI01
I:4-41,I:63-78,I:211-289,I:403-463
1j
1ojdL01
L:4-41,L:63-78,L:211-289,L:403-463
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Polyamine Oxidase; Chain A, domain 2
(62)
Homologous Superfamily
:
[code=3.90.660.10, no name defined]
(61)
Human (Homo sapiens)
(29)
2a
1ojdA02
A:42-62,A:79-107,A:200-210,A:290-402
2b
1ojdB02
B:42-62,B:79-107,B:200-210,B:290-402
2c
1ojdC02
C:42-62,C:79-107,C:200-210,C:290-402
2d
1ojdD02
D:42-62,D:79-107,D:200-210,D:290-402
2e
1ojdE02
E:42-62,E:79-107,E:200-210,E:290-402
2f
1ojdF02
F:42-62,F:79-107,F:200-210,F:290-402
2g
1ojdG02
G:42-62,G:79-107,G:200-210,G:290-402
2h
1ojdH02
H:42-62,H:79-107,H:200-210,H:290-402
2i
1ojdI02
I:42-62,I:79-107,I:200-210,I:290-402
2j
1ojdL02
L:42-62,L:79-107,L:200-210,L:290-402
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Guanine Nucleotide Dissociation Inhibitor; domain 1
(50)
Homologous Superfamily
:
Guanine Nucleotide Dissociation Inhibitor, domain 1
(50)
Human (Homo sapiens)
(29)
3a
1ojdA03
A:108-199
3b
1ojdB03
B:108-199
3c
1ojdC03
C:108-199
3d
1ojdD03
D:108-199
3e
1ojdE03
E:108-199
3f
1ojdF03
F:108-199
3g
1ojdG03
G:108-199
3h
1ojdH03
H:108-199
3i
1ojdI03
I:108-199
3j
1ojdL03
L:108-199
[
close CATH info
]
Pfam Domains
(1, 10)
Info
all PFAM domains
1a: PFAM_Amino_oxidase_1ojdL01 (L:14-451)
1b: PFAM_Amino_oxidase_1ojdL02 (L:14-451)
1c: PFAM_Amino_oxidase_1ojdL03 (L:14-451)
1d: PFAM_Amino_oxidase_1ojdL04 (L:14-451)
1e: PFAM_Amino_oxidase_1ojdL05 (L:14-451)
1f: PFAM_Amino_oxidase_1ojdL06 (L:14-451)
1g: PFAM_Amino_oxidase_1ojdL07 (L:14-451)
1h: PFAM_Amino_oxidase_1ojdL08 (L:14-451)
1i: PFAM_Amino_oxidase_1ojdL09 (L:14-451)
1j: PFAM_Amino_oxidase_1ojdL10 (L:14-451)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Amino_oxidase
(60)
Homo sapiens (Human)
(37)
1a
Amino_oxidase-1ojdL01
L:14-451
1b
Amino_oxidase-1ojdL02
L:14-451
1c
Amino_oxidase-1ojdL03
L:14-451
1d
Amino_oxidase-1ojdL04
L:14-451
1e
Amino_oxidase-1ojdL05
L:14-451
1f
Amino_oxidase-1ojdL06
L:14-451
1g
Amino_oxidase-1ojdL07
L:14-451
1h
Amino_oxidase-1ojdL08
L:14-451
1i
Amino_oxidase-1ojdL09
L:14-451
1j
Amino_oxidase-1ojdL10
L:14-451
[
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 (814 KB)
Header - Asym.Unit
Biol.Unit 1 (170 KB)
Header - Biol.Unit 1
Biol.Unit 2 (171 KB)
Header - Biol.Unit 2
Biol.Unit 3 (171 KB)
Header - Biol.Unit 3
Biol.Unit 4 (171 KB)
Header - Biol.Unit 4
Biol.Unit 5 (170 KB)
Header - Biol.Unit 5
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
1OJD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help