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.
3WD7
Asym. Unit
Info
Asym.Unit (140 KB)
Biol.Unit 1 (134 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TYPE III POLYKETIDE SYNTHASE
Authors
:
T. Mori, Y. Shimokawa, T. Matsui, R. Kato, S. Sugio, H. Morita, I. Abe
Date
:
10 Jun 13 (Deposition) - 04 Sep 13 (Release) - 04 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Acridone Synthase, Type Iii Polyketide Synthase, Acyltransferase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Mori, Y. Shimokawa, T. Matsui, K. Kinjo, R. Kato, H. Noguchi, S. Sugio, H. Morita, I. Abe
Cloning, Characterization, And Crystal Structure Analysis O Novel Type Iii Polyketide Synthases From Citrus Microcarpa
To Be Published
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: COENZYME A (COAa)
1b: COENZYME A (COAb)
2a: NICKEL (II) ION (NIa)
2b: NICKEL (II) ION (NIb)
2c: NICKEL (II) ION (NIc)
2d: NICKEL (II) ION (NId)
2e: NICKEL (II) ION (NIe)
2f: NICKEL (II) ION (NIf)
2g: NICKEL (II) ION (NIg)
2h: NICKEL (II) ION (NIh)
2i: NICKEL (II) ION (NIi)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
2
Ligand/Ion
COENZYME A
2
NI
9
Ligand/Ion
NICKEL (II) ION
3
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:59 , LYS A:62 , CYS A:164 , ASP A:207 , VAL A:210 , LEU A:267 , LYS A:268 , LYS A:269 , VAL A:271 , GLY A:305 , GLY A:306 , PRO A:307 , ALA A:308 , HOH A:603 , HOH A:648 , HOH A:652 , HOH A:682
BINDING SITE FOR RESIDUE COA A 401
02
AC2
SOFTWARE
HIS A:205 , ASP A:207 , HIS A:266 , HOH A:635 , HOH A:643
BINDING SITE FOR RESIDUE NI A 402
03
AC3
SOFTWARE
HIS A:329 , GLU A:333 , HOH A:580 , HOH A:602 , HOH A:666
BINDING SITE FOR RESIDUE NI A 403
04
AC4
SOFTWARE
HIS A:-2 , HOH A:568 , HOH A:609 , HIS B:-4 , HIS B:-6 , GLU B:5
BINDING SITE FOR RESIDUE NI A 404
05
AC5
SOFTWARE
HIS A:-3 , HIS B:-5 , HIS B:-7 , MET B:-11
BINDING SITE FOR RESIDUE NI A 405
06
AC6
SOFTWARE
HIS A:-7 , MET A:-11 , HOH A:675 , HIS B:-2
BINDING SITE FOR RESIDUE NI A 406
07
AC7
SOFTWARE
HIS A:-5 , HOH A:553 , HOH A:627 , HOH A:669 , HIS B:-3
BINDING SITE FOR RESIDUE NI A 407
08
AC8
SOFTWARE
HIS A:-6 , HIS A:-4 , HOH A:594 , HOH A:668
BINDING SITE FOR RESIDUE NI A 408
09
AC9
SOFTWARE
HIS A:-3 , HIS A:-4
BINDING SITE FOR RESIDUE SO4 A 409
10
BC1
SOFTWARE
LYS B:55 , LEU B:59 , LYS B:62 , ASP B:207 , VAL B:210 , LEU B:267 , LYS B:268 , VAL B:271 , GLY B:306 , PRO B:307 , ALA B:308 , PHE B:373 , HOH B:649
BINDING SITE FOR RESIDUE COA B 401
11
BC2
SOFTWARE
HIS B:329 , GLU B:333 , HOH B:604 , HOH B:616 , HOH B:638
BINDING SITE FOR RESIDUE NI B 402
12
BC3
SOFTWARE
HIS B:205 , ASP B:207 , HIS B:266 , HOH B:532 , HOH B:565
BINDING SITE FOR RESIDUE NI B 403
13
BC4
SOFTWARE
HOH A:553 , HIS B:-6 , HIS B:-5
BINDING SITE FOR RESIDUE SO4 B 404
14
BC5
SOFTWARE
HIS B:-3 , HIS B:-2 , HIS B:-4 , MET B:1 , HOH B:555 , HOH B:634
BINDING SITE FOR RESIDUE SO4 B 405
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3wd7a1 (A:-11-235)
1b: SCOP_d3wd7a2 (A:236-389)
1c: SCOP_d3wd7b1 (B:-11-235)
1d: SCOP_d3wd7b2 (B:236-389)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiolase-like
(231)
Superfamily
:
Thiolase-like
(231)
Family
:
automated matches
(108)
Protein domain
:
automated matches
(108)
Citrus microcarpa [TaxId: 164113]
(2)
1a
d3wd7a1
A:-11-235
1b
d3wd7a2
A:236-389
1c
d3wd7b1
B:-11-235
1d
d3wd7b2
B:236-389
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 (140 KB)
Header - Asym.Unit
Biol.Unit 1 (134 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
3WD7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
