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.
4KWD
Asym. Unit
Info
Asym.Unit (231 KB)
Biol.Unit 1 (117 KB)
Biol.Unit 2 (111 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 ASPERGILLUS TERREUS ARISTOLOCHENE SYNTHASE COMPLEXED WITH (1R,8R,9AS)-1,9A-DIMETHYL-8-(PROP-1-EN-2-YL) DECAHYDROQUINOLIZIN-5-IUM
Authors
:
M. Chen, N. Al-Lami, M. Janvier, E. L. D'Antonio, J. A. Faraldos, D. E. Ca R. K. Allemann, D. W. Christianson
Date
:
23 May 13 (Deposition) - 14 Aug 13 (Release) - 28 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.86
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Class I Terpene Cyclase, Metal-Binding Motif, Farnesyl Diphosphate, Alpha-Helical Fold, Lyase-Lyase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Chen, N. Al-Lami, M. Janvier, E. L. D'Antonio, J. A. Faraldos, D. E. Cane, R. K. Allemann, D. W. Christianson
Mechanistic Insights From The Binding Of Substrate And Carbocation Intermediate Analogues To Aristolochene Synthase.
Biochemistry V. 52 5441 2013
[
close entry info
]
Hetero Components
(4, 22)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: (1R,5R,8R,9AS)-1,9A-DIMETHYL-8-(PR... (JF2a)
2b: (1R,5R,8R,9AS)-1,9A-DIMETHYL-8-(PR... (JF2b)
2c: (1R,5R,8R,9AS)-1,9A-DIMETHYL-8-(PR... (JF2c)
2d: (1R,5R,8R,9AS)-1,9A-DIMETHYL-8-(PR... (JF2d)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
4a: PYROPHOSPHATE 2- (POPa)
4b: PYROPHOSPHATE 2- (POPb)
4c: PYROPHOSPHATE 2- (POPc)
4d: PYROPHOSPHATE 2- (POPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
JF2
4
Ligand/Ion
(1R,5R,8R,9AS)-1,9A-DIMETHYL-8-(PROP-1-EN-2-YL)OCTAHYDRO-2H-QUINOLIZINIUM
3
MG
12
Ligand/Ion
MAGNESIUM ION
4
POP
4
Ligand/Ion
PYROPHOSPHATE 2-
[
close Hetero Component info
]
Sites
(22, 22)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:84 , ARG A:169 , ASN A:213 , SER A:217 , LYS A:220 , GLU A:221 , ARG A:308 , TYR A:309 , MG A:402 , MG A:403 , MG A:404 , JF2 A:405 , HOH A:810 , HOH A:811 , HOH A:812 , HOH A:820 , HOH A:822 , HOH A:823 , HOH A:825 , HOH A:835
BINDING SITE FOR RESIDUE POP A 401
02
AC2
SOFTWARE
ASP A:84 , POP A:401 , MG A:403 , HOH A:812 , HOH A:823 , HOH A:824 , HOH A:825
BINDING SITE FOR RESIDUE MG A 402
03
AC3
SOFTWARE
ASP A:84 , POP A:401 , MG A:402 , HOH A:810 , HOH A:811 , HOH A:812
BINDING SITE FOR RESIDUE MG A 403
04
AC4
SOFTWARE
ASN A:213 , SER A:217 , GLU A:221 , POP A:401 , HOH A:820
BINDING SITE FOR RESIDUE MG A 404
05
AC5
SOFTWARE
TYR A:61 , PHE A:81 , VAL A:173 , LEU A:178 , LEU A:209 , ASN A:213 , ASN A:299 , POP A:401 , HOH A:835
BINDING SITE FOR RESIDUE JF2 A 405
06
AC6
SOFTWARE
ASP B:84 , MG B:702 , POP B:704 , HOH B:1122 , HOH B:1130 , HOH B:1134 , HOH B:1150
BINDING SITE FOR RESIDUE MG B 701
07
AC7
SOFTWARE
ASP B:84 , MG B:701 , POP B:704 , HOH B:1122 , HOH B:1151 , HOH B:1152
BINDING SITE FOR RESIDUE MG B 702
08
AC8
SOFTWARE
ASN B:213 , SER B:217 , GLU B:221 , POP B:704 , HOH B:1129
BINDING SITE FOR RESIDUE MG B 703
09
AC9
SOFTWARE
PHE B:81 , ASP B:84 , ARG B:169 , ASN B:213 , SER B:217 , LYS B:220 , GLU B:221 , ARG B:308 , TYR B:309 , MG B:701 , MG B:702 , MG B:703 , JF2 B:705 , HOH B:1122 , HOH B:1128 , HOH B:1129 , HOH B:1130 , HOH B:1134 , HOH B:1151 , HOH B:1152 , HOH B:1153
BINDING SITE FOR RESIDUE POP B 704
10
BC1
SOFTWARE
TYR B:61 , PHE B:81 , PHE B:147 , VAL B:173 , LEU B:178 , LEU B:209 , ASN B:213 , POP B:704 , HOH B:1153
BINDING SITE FOR RESIDUE JF2 B 705
11
BC2
SOFTWARE
ARG B:107 , GLU B:142 , ARG B:149 , ARG C:197 , LEU C:275 , HOH C:629 , HOH C:631 , HOH C:634
BINDING SITE FOR RESIDUE GOL B 706
12
BC3
SOFTWARE
ASP C:84 , ARG C:169 , ASN C:213 , SER C:217 , LYS C:220 , GLU C:221 , ARG C:308 , TYR C:309 , MG C:402 , MG C:403 , MG C:404 , JF2 C:405 , HOH C:709 , HOH C:711 , HOH C:713 , HOH C:715 , HOH C:716 , HOH C:718 , HOH C:729
BINDING SITE FOR RESIDUE POP C 401
13
BC4
SOFTWARE
ASP C:84 , POP C:401 , MG C:403 , HOH C:709 , HOH C:711 , HOH C:713
BINDING SITE FOR RESIDUE MG C 402
14
BC5
SOFTWARE
ASP C:84 , POP C:401 , MG C:402 , HOH C:713 , HOH C:714 , HOH C:715 , HOH C:718
BINDING SITE FOR RESIDUE MG C 403
15
BC6
SOFTWARE
ARG C:169 , ASN C:213 , SER C:217 , GLU C:221 , POP C:401 , HOH C:717
BINDING SITE FOR RESIDUE MG C 404
16
BC7
SOFTWARE
TYR C:61 , PHE C:81 , VAL C:173 , LEU C:178 , LEU C:209 , ASN C:213 , ASN C:299 , POP C:401 , HOH C:729
BINDING SITE FOR RESIDUE JF2 C 405
17
BC8
SOFTWARE
ARG B:197 , LEU B:275 , HOH B:1027 , ARG C:107 , GLU C:142 , ARG C:149
BINDING SITE FOR RESIDUE GOL C 406
18
BC9
SOFTWARE
PHE D:81 , ASP D:84 , ARG D:169 , ASN D:213 , SER D:217 , LYS D:220 , GLU D:221 , ARG D:308 , TYR D:309 , MG D:402 , MG D:403 , MG D:404 , JF2 D:405 , HOH D:612 , HOH D:618 , HOH D:619 , HOH D:621 , HOH D:622 , HOH D:623 , HOH D:625
BINDING SITE FOR RESIDUE POP D 401
19
CC1
SOFTWARE
ASP D:84 , POP D:401 , MG D:403 , HOH D:605 , HOH D:619 , HOH D:622 , HOH D:625
BINDING SITE FOR RESIDUE MG D 402
20
CC2
SOFTWARE
ASP D:84 , POP D:401 , MG D:402 , HOH D:612 , HOH D:622 , HOH D:623
BINDING SITE FOR RESIDUE MG D 403
21
CC3
SOFTWARE
ASN D:213 , SER D:217 , GLU D:221 , POP D:401 , HOH D:621
BINDING SITE FOR RESIDUE MG D 404
22
CC4
SOFTWARE
TYR D:61 , PHE D:81 , PHE D:147 , VAL D:173 , LEU D:178 , ASN D:213 , ASN D:299 , POP D:401
BINDING SITE FOR RESIDUE JF2 D 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_d4kwda_ (A:)
1b: SCOP_d4kwdb_ (B:)
1c: SCOP_d4kwdc_ (C:)
1d: SCOP_d4kwdd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Terpenoid synthases
(196)
Superfamily
:
Terpenoid synthases
(196)
Family
:
Aristolochene/pentalenene synthase
(16)
Protein domain
:
automated matches
(11)
Aspergillus terreus [TaxId: 33178]
(11)
1a
d4kwda_
A:
1b
d4kwdb_
B:
1c
d4kwdc_
C:
1d
d4kwdd_
D:
[
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
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 (231 KB)
Header - Asym.Unit
Biol.Unit 1 (117 KB)
Header - Biol.Unit 1
Biol.Unit 2 (111 KB)
Header - Biol.Unit 2
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
4KWD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help