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.
1YQD
Asym. Unit
Info
Asym.Unit (128 KB)
Biol.Unit 1 (123 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
SINAPYL ALCOHOL DEHYDROGENASE COMPLEXED WITH NADP+
Authors
:
E. K. Bomati, J. P. Noel
Date
:
01 Feb 05 (Deposition) - 12 Jul 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Lignin, Monolignol, Oxidoreductase, Zinc-Dependent, Plant Defense, Biosynthesis, Substrate Inhibition, Medium-Chain Dehydrogense/Reductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. K. Bomati, J. P. Noel
Structural And Kinetic Basis For Substrate Selectivity In Populus Tremuloides Sinapyl Alcohol Dehydrogenase.
Plant Cell V. 17 1598 2005
[
close entry info
]
Hetero Components
(4, 9)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
1b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
2a: GLYCEROL (GOLa)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
3b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTT
2
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
2
GOL
1
Ligand/Ion
GLYCEROL
3
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:50 , SER A:52 , HIS A:72 , CYS A:166 , NAP A:500 , HOH A:2046
BINDING SITE FOR RESIDUE ZN A 1000
2
AC2
SOFTWARE
CYS A:103 , CYS A:106 , CYS A:109 , CYS A:117
BINDING SITE FOR RESIDUE ZN A 2000
3
AC3
SOFTWARE
CYS B:103 , CYS B:106 , CYS B:109 , CYS B:117
BINDING SITE FOR RESIDUE ZN B 3000
4
AC4
SOFTWARE
CYS B:50 , SER B:52 , HIS B:72 , CYS B:166 , NAP B:600 , HOH B:4083
BINDING SITE FOR RESIDUE ZN B 4000
5
AC5
SOFTWARE
HIS A:51 , SER A:52 , HIS A:55 , TRP A:61 , CYS A:166 , THR A:170 , GLY A:191 , LEU A:192 , GLY A:193 , GLY A:194 , LEU A:195 , SER A:214 , THR A:215 , SER A:216 , LYS A:219 , THR A:254 , VAL A:255 , SER A:256 , ALA A:257 , VAL A:277 , GLY A:278 , ALA A:279 , SER A:301 , GLY A:302 , ILE A:303 , ASN A:343 , ARG A:348 , DTT A:700 , ZN A:1000 , HOH A:2002 , HOH A:2007 , HOH A:2043 , HOH A:2046 , HOH A:2148 , HOH A:2150 , HOH A:2167 , ILE B:292
BINDING SITE FOR RESIDUE NAP A 500
6
AC6
SOFTWARE
ILE A:292 , CYS B:50 , HIS B:51 , SER B:52 , HIS B:55 , TRP B:61 , CYS B:166 , THR B:170 , GLY B:191 , LEU B:192 , GLY B:193 , GLY B:194 , LEU B:195 , SER B:214 , THR B:215 , SER B:216 , LYS B:219 , THR B:254 , VAL B:255 , SER B:256 , ALA B:257 , VAL B:277 , GLY B:278 , ALA B:279 , SER B:301 , GLY B:302 , ILE B:303 , ASN B:343 , ARG B:348 , DTT B:800 , ZN B:4000 , HOH B:4003 , HOH B:4007 , HOH B:4036 , HOH B:4083 , HOH B:4135 , HOH B:4152
BINDING SITE FOR RESIDUE NAP B 600
7
AC7
SOFTWARE
SER A:52 , TRP A:61 , HIS A:72 , CYS A:98 , NAP A:500 , HOH A:2046 , HOH A:2149
BINDING SITE FOR RESIDUE DTT A 700
8
AC8
SOFTWARE
ILE A:292 , SER B:52 , HIS B:72 , CYS B:98 , NAP B:600 , HOH B:4083 , HOH B:4137
BINDING SITE FOR RESIDUE DTT B 800
9
AC9
SOFTWARE
HOH A:2090 , LEU B:268 , SER B:270 , LYS B:296 , HOH B:4085 , HOH B:4123
BINDING SITE FOR RESIDUE GOL B 900
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1yqdA02 (A:167-323)
1b: CATH_1yqdB02 (B:167-323)
2a: CATH_1yqdA01 (A:4-166,A:324-362)
2b: CATH_1yqdB01 (B:4-166,B:324-362)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Quaking aspen (Populus tremuloides)
(2)
1a
1yqdA02
A:167-323
1b
1yqdB02
B:167-323
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Quaking aspen (Populus tremuloides)
(2)
2a
1yqdA01
A:4-166,A:324-362
2b
1yqdB01
B:4-166,B:324-362
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_ADH_N_1yqdB01 (B:37-152)
1b: PFAM_ADH_N_1yqdB02 (B:37-152)
2a: PFAM_ADH_zinc_N_1yqdB03 (B:194-318)
2b: PFAM_ADH_zinc_N_1yqdB04 (B:194-318)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GroES
(70)
Family
:
ADH_N
(62)
Populus tremuloides (Quaking aspen)
(2)
1a
ADH_N-1yqdB01
B:37-152
1b
ADH_N-1yqdB02
B:37-152
Clan
:
NADP_Rossmann
(1239)
Family
:
ADH_zinc_N
(75)
Populus tremuloides (Quaking aspen)
(2)
2a
ADH_zinc_N-1yqdB03
B:194-318
2b
ADH_zinc_N-1yqdB04
B:194-318
[
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 (128 KB)
Header - Asym.Unit
Biol.Unit 1 (123 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
1YQD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help