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.
3IWK
Biol. Unit 2
Info
Asym.Unit (973 KB)
Biol.Unit 1 (171 KB)
Biol.Unit 2 (170 KB)
Biol.Unit 3 (170 KB)
Biol.Unit 4 (173 KB)
Biol.Unit 5 (173 KB)
Biol.Unit 6 (174 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 AMINOALDEHYDE DEHYDROGENASE 1 FROM PISUM SATIVUM (PSAMADH1)
Authors
:
D. Kopecny, S. Morera, P. Briozzo
Date
:
02 Sep 09 (Deposition) - 19 Jan 10 (Release) - 04 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,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,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Rossmann Fold, Dimer, Aminoaldehyde Dehydrogenase, Betaine Aldehyde Dehydrogenase, Nad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Tylichova, D. Kopecny, S. Morera, P. Briozzo, R. Lenobel, J. Snegaroff, M. Sebela
Structural And Functional Characterization Of Plant Aminoaldehyde Dehydrogenase From Pisum Sativum With A Broad Specificity For Natural And Synthetic Aminoaldehydes.
J. Mol. Biol. V. 396 870 2010
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
2a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
4d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
4e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
4f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
4g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
4h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
4i: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADi)
4j: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADj)
4k: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADk)
4l: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADl)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
4f: SODIUM ION (NAf)
4g: SODIUM ION (NAg)
4h: SODIUM ION (NAh)
4i: SODIUM ION (NAi)
4j: SODIUM ION (NAj)
4k: SODIUM ION (NAk)
4l: SODIUM ION (NAl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
MRD
1
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
3
NA
-1
Ligand/Ion
SODIUM ION
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
ASN C:27 , ILE C:28 , ASP C:99 , LEU C:189
BINDING SITE FOR RESIDUE NA C 504
2
AC8
SOFTWARE
PRO C:160 , TRP C:161 , GLU C:188 , GLY C:218 , GLY C:222 , ALA C:223 , GLY C:238 , SER C:239 , THR C:242 , LYS C:245 , ILE C:246 , GLY C:262 , CYS C:294 , GLN C:341 , LYS C:344 , GLU C:393 , PHE C:395 , HOH C:1327
BINDING SITE FOR RESIDUE NAD C 505
3
AC9
SOFTWARE
TYR C:163 , MET C:167 , TRP C:170 , ILE C:293 , CYS C:294 , SER C:295 , TRP C:459 , HOH C:1671
BINDING SITE FOR RESIDUE GOL C 2003
4
BC1
SOFTWARE
ASN D:27 , ASP D:99 , LEU D:189
BINDING SITE FOR RESIDUE NA D 504
5
BC2
SOFTWARE
GLY D:218 , HIS D:219 , GLY D:222 , ALA D:223 , SER D:239 , THR D:242 , LYS D:245 , ILE D:246
BINDING SITE FOR RESIDUE NAD D 505
6
BC3
SOFTWARE
ASN D:162 , TYR D:163 , MET D:167 , ILE D:293 , CYS D:294 , GLN D:451 , SER D:453 , TRP D:459
BINDING SITE FOR RESIDUE MRD D 2004
[
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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3iwka_ (A:)
1b: SCOP_d3iwki_ (I:)
1c: SCOP_d3iwkj_ (J:)
1d: SCOP_d3iwkk_ (K:)
1e: SCOP_d3iwkl_ (L:)
1f: SCOP_d3iwkb_ (B:)
1g: SCOP_d3iwkc_ (C:)
1h: SCOP_d3iwkd_ (D:)
1i: SCOP_d3iwke_ (E:)
1j: SCOP_d3iwkf_ (F:)
1k: SCOP_d3iwkg_ (G:)
1l: SCOP_d3iwkh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ALDH-like
(168)
Superfamily
:
ALDH-like
(168)
Family
:
automated matches
(88)
Protein domain
:
automated matches
(88)
Pea (Pisum sativum) [TaxId: 3888]
(2)
1a
d3iwka_
A:
1b
d3iwki_
I:
1c
d3iwkj_
J:
1d
d3iwkk_
K:
1e
d3iwkl_
L:
1f
d3iwkb_
B:
1g
d3iwkc_
C:
1h
d3iwkd_
D:
1i
d3iwke_
E:
1j
d3iwkf_
F:
1k
d3iwkg_
G:
1l
d3iwkh_
H:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3iwkA02 (A:263-454)
1b: CATH_3iwkI02 (I:263-454)
1c: CATH_3iwkJ02 (J:263-454)
1d: CATH_3iwkK02 (K:263-454)
1e: CATH_3iwkL02 (L:263-454)
1f: CATH_3iwkB02 (B:263-454)
1g: CATH_3iwkC02 (C:263-454)
1h: CATH_3iwkD02 (D:263-454)
1i: CATH_3iwkE02 (E:263-454)
1j: CATH_3iwkF02 (F:263-454)
1k: CATH_3iwkG02 (G:263-454)
1l: CATH_3iwkH02 (H:263-454)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Garden pea (Pisum sativum)
(2)
1a
3iwkA02
A:263-454
1b
3iwkI02
I:263-454
1c
3iwkJ02
J:263-454
1d
3iwkK02
K:263-454
1e
3iwkL02
L:263-454
1f
3iwkB02
B:263-454
1g
3iwkC02
C:263-454
1h
3iwkD02
D:263-454
1i
3iwkE02
E:263-454
1j
3iwkF02
F:263-454
1k
3iwkG02
G:263-454
1l
3iwkH02
H:263-454
[
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 C
Chain D
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 (973 KB)
Header - Asym.Unit
Biol.Unit 1 (171 KB)
Header - Biol.Unit 1
Biol.Unit 2 (170 KB)
Header - Biol.Unit 2
Biol.Unit 3 (170 KB)
Header - Biol.Unit 3
Biol.Unit 4 (173 KB)
Header - Biol.Unit 4
Biol.Unit 5 (173 KB)
Header - Biol.Unit 5
Biol.Unit 6 (174 KB)
Header - Biol.Unit 6
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
3IWK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help