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.
3D3W
Asym. Unit
Info
Asym.Unit (94 KB)
Biol.Unit 1 (173 KB)
Biol.Unit 2 (88 KB)
Biol.Unit 3 (90 KB)
Biol.Unit 4 (87 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 L-XYLULOSE REDUCTASE WITH BOUND COENZYME, PHOSPHATE AND HYDROXIDE.
Authors
:
H. -T. Zhao, O. El-Kabbani
Date
:
12 May 08 (Deposition) - 21 Apr 09 (Release) - 28 Jul 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.87
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: A (2x)
Biol. Unit 4: B (2x)
Keywords
:
L-Xylulose Reductase, Uronate Cycle, Short-Chain Dehydrogenase/Reductase(Sdr) Superfamily, Glucose Metabolism, Acetylation, Carbohydrate Metabolism, Membrane, Nadp, Oxidoreductase, Xylose Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. T. Zhao, S. Endo, S. Ishikura, R. Chung, P. J. Hogg, A. Hara, O. El-Kabbani
Structure/Function Analysis Of A Critical Disulfide Bond In The Active Site Of L-Xylulose Reductase.
Cell. Mol. Life Sci. V. 66 1570 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
1b: S-HYDROXYCYSTEINE (CSOb)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
3a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
2
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:14 , GLY A:16 , LYS A:17 , GLY A:18 , ILE A:19 , SER A:38 , ARG A:39 , THR A:40 , ASP A:43 , VAL A:59 , ASP A:60 , LEU A:61 , GLY A:62 , ASN A:83 , ALA A:84 , ALA A:85 , VAL A:86 , ARG A:102 , VAL A:106 , VAL A:134 , SER A:135 , SER A:136 , TYR A:149 , LYS A:153 , PRO A:179 , THR A:180 , VAL A:182 , THR A:184 , SER A:185 , MET A:186 , GLY A:187 , HOH A:259 , HOH A:263 , HOH A:270 , HOH A:295 , HOH A:297 , HOH A:367
BINDING SITE FOR RESIDUE NAP A 245
2
AC2
SOFTWARE
GLY B:14 , GLY B:16 , LYS B:17 , GLY B:18 , ILE B:19 , SER B:38 , ARG B:39 , THR B:40 , ASP B:43 , VAL B:59 , ASP B:60 , LEU B:61 , GLY B:62 , ASN B:83 , ALA B:84 , ALA B:85 , ARG B:102 , VAL B:106 , VAL B:134 , SER B:135 , SER B:136 , TYR B:149 , LYS B:153 , PRO B:179 , THR B:180 , VAL B:181 , VAL B:182 , THR B:184 , SER B:185 , GLY B:187 , PO4 B:245 , HOH B:1250 , HOH B:1281 , HOH B:1307 , HOH B:1319 , HOH B:1345 , HOH B:1362 , HOH B:1410 , HOH B:1439
BINDING SITE FOR RESIDUE NAP B 1245
3
AC3
SOFTWARE
SER B:136 , GLN B:137 , CYS B:138 , PRO B:179 , THR B:180 , VAL B:181 , MET B:200 , NAP B:1245 , HOH B:1439
BINDING SITE FOR RESIDUE PO4 B 245
[
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: ADH_SHORT (A:136-164,B:136-164)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_SHORT
PS00061
Short-chain dehydrogenases/reductases family signature.
DCXR_HUMAN
136-164
2
A:136-164
B:136-164
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1 (A:1-18 | B:1-18)
Exon 1.2 (A:18-50 | B:18-50)
Exon 1.3 (A:51-102 | B:51-102)
Exon 1.4 (A:102-116 | B:102-116)
Exon 1.5 (A:117-150 | B:117-150)
Exon 1.6 (A:150-171 | B:150-171)
Exon 1.7 (A:172-211 | B:172-211)
Exon 1.8 (A:211-244 | B:211-244)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/1.8
9: Boundary 1.8/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000306869
1
ENSE00001155492
chr17:
79995573-79995507
67
DCXR_HUMAN
1-18
18
2
A:1-18
B:1-18
18
18
1.2
ENST00000306869
2
ENSE00001164074
chr17:
79995423-79995326
98
DCXR_HUMAN
18-50
33
2
A:18-50
B:18-50
33
33
1.3
ENST00000306869
3
ENSE00001164069
chr17:
79994889-79994735
155
DCXR_HUMAN
51-102
52
2
A:51-102
B:51-102
52
52
1.4
ENST00000306869
4
ENSE00001164064
chr17:
79994639-79994597
43
DCXR_HUMAN
102-116
15
2
A:102-116
B:102-116
15
15
1.5
ENST00000306869
5
ENSE00001164060
chr17:
79994519-79994420
100
DCXR_HUMAN
117-150
34
2
A:117-150
B:117-150
34
34
1.6
ENST00000306869
6
ENSE00001164055
chr17:
79994324-79994260
65
DCXR_HUMAN
150-171
22
2
A:150-171
B:150-171
22
22
1.7
ENST00000306869
7
ENSE00001164049
chr17:
79994184-79994067
118
DCXR_HUMAN
172-211
40
2
A:172-211
B:172-211
40
40
1.8
ENST00000306869
8
ENSE00001300238
chr17:
79993939-79993757
183
DCXR_HUMAN
211-244
34
2
A:211-244
B:211-244
34
34
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3d3wa_ (A:)
1b: SCOP_d3d3wb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
automated matches
(114)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d3d3wa_
A:
1b
d3d3wb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3d3wA00 (A:1-244)
1b: CATH_3d3wB00 (B:1-244)
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)
Human (Homo sapiens)
(188)
1a
3d3wA00
A:1-244
1b
3d3wB00
B:1-244
[
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 (94 KB)
Header - Asym.Unit
Biol.Unit 1 (173 KB)
Header - Biol.Unit 1
Biol.Unit 2 (88 KB)
Header - Biol.Unit 2
Biol.Unit 3 (90 KB)
Header - Biol.Unit 3
Biol.Unit 4 (87 KB)
Header - Biol.Unit 4
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
3D3W
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help