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.
1W8S
Asym. Unit
Info
Asym.Unit (423 KB)
Biol.Unit 1 (211 KB)
Biol.Unit 2 (212 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE MECHANISM OF THE SCHIFF BASE FORMING FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE: STRUCTURAL ANALYSIS OF REACTION INTERMEDIATES
Authors
:
E. Lorentzen, R. Hensel, B. Siebers, E. Pohl
Date
:
27 Sep 04 (Deposition) - 23 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Keywords
:
Aldolase, Fructose 1, 6-Bisphosphate, Tim Barrel, Glycolytic, Archaeal, Catalytic Mechanism, Reaction Intermediate, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Lorentzen, B. Siebers, R. Hensel, E. Pohl
Mechanism Of The Schiff Base Forming Fructose-1, 6-Bisphosphate Aldolase: Structural Analysis Of Reaction Intermediates
Biochemistry V. 44 4222 2005
[
close entry info
]
Hetero Components
(1, 10)
Info
All Hetero Components
1a: FRUCTOSE-1,6-DIPHOSPHATE (FBPa)
1b: FRUCTOSE-1,6-DIPHOSPHATE (FBPb)
1c: FRUCTOSE-1,6-DIPHOSPHATE (FBPc)
1d: FRUCTOSE-1,6-DIPHOSPHATE (FBPd)
1e: FRUCTOSE-1,6-DIPHOSPHATE (FBPe)
1f: FRUCTOSE-1,6-DIPHOSPHATE (FBPf)
1g: FRUCTOSE-1,6-DIPHOSPHATE (FBPg)
1h: FRUCTOSE-1,6-DIPHOSPHATE (FBPh)
1i: FRUCTOSE-1,6-DIPHOSPHATE (FBPi)
1j: FRUCTOSE-1,6-DIPHOSPHATE (FBPj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FBP
10
Ligand/Ion
FRUCTOSE-1,6-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:22 , ASP A:24 , HIS A:25 , GLU A:28 , HIS A:29 , ARG A:148 , LYS A:177 , LYS A:179 , SER A:202 , GLY A:203 , GLY A:204 , ALA A:229 , VAL A:230 , GLY A:231 , ARG A:232 , HOH A:2114 , HOH A:2116 , HOH A:2139
BINDING SITE FOR RESIDUE FBP A 270
02
AC2
SOFTWARE
ASP B:24 , HIS B:25 , GLU B:28 , HIS B:29 , ARG B:148 , LYS B:177 , LYS B:179 , SER B:202 , GLY B:203 , GLY B:204 , ALA B:229 , VAL B:230 , GLY B:231 , ARG B:232 , HOH B:2123 , HOH B:2151 , HOH B:2152 , HOH B:2153 , HOH B:2154
BINDING SITE FOR RESIDUE FBP B 270
03
AC3
SOFTWARE
ASP C:24 , HIS C:25 , GLU C:28 , HIS C:29 , ARG C:148 , LYS C:177 , LYS C:179 , SER C:202 , GLY C:203 , GLY C:204 , ALA C:229 , VAL C:230 , GLY C:231 , ARG C:232 , HOH C:2056 , HOH C:2108 , HOH C:2118 , HOH C:2119
BINDING SITE FOR RESIDUE FBP C 270
04
AC4
SOFTWARE
ALA D:22 , ASP D:24 , HIS D:25 , GLU D:28 , HIS D:29 , ARG D:148 , LYS D:177 , LYS D:179 , SER D:202 , GLY D:203 , GLY D:204 , VAL D:230 , GLY D:231 , ARG D:232 , HOH D:2096 , HOH D:2109 , HOH D:2110 , HOH D:2111
BINDING SITE FOR RESIDUE FBP D 270
05
AC5
SOFTWARE
ALA E:22 , ASP E:24 , HIS E:25 , GLU E:28 , HIS E:29 , ARG E:148 , LYS E:177 , LYS E:179 , SER E:202 , GLY E:203 , GLY E:204 , ALA E:229 , VAL E:230 , GLY E:231 , ARG E:232 , HOH E:2010 , HOH E:2121 , HOH E:2133 , HOH E:2134 , HOH E:2135
BINDING SITE FOR RESIDUE FBP E 270
06
AC6
SOFTWARE
ALA F:22 , ASP F:24 , HIS F:25 , GLU F:28 , HIS F:29 , ARG F:148 , LYS F:177 , LYS F:179 , SER F:202 , GLY F:203 , GLY F:204 , ALA F:229 , VAL F:230 , GLY F:231 , ARG F:232 , HOH F:2107 , HOH F:2115
BINDING SITE FOR RESIDUE FBP F 270
07
AC7
SOFTWARE
ALA G:22 , ASP G:24 , HIS G:25 , GLU G:28 , HIS G:29 , ARG G:148 , LYS G:177 , LYS G:179 , SER G:202 , GLY G:203 , GLY G:204 , ALA G:229 , VAL G:230 , GLY G:231 , ARG G:232 , HOH G:2117 , HOH G:2132 , HOH G:2133
BINDING SITE FOR RESIDUE FBP G 270
08
AC8
SOFTWARE
ALA H:22 , ASP H:24 , HIS H:25 , GLU H:28 , HIS H:29 , ARG H:148 , LYS H:177 , LYS H:179 , SER H:202 , GLY H:203 , GLY H:204 , ALA H:229 , VAL H:230 , GLY H:231 , ARG H:232 , HOH H:2075 , HOH H:2134 , HOH H:2147
BINDING SITE FOR RESIDUE FBP H 270
09
AC9
SOFTWARE
ALA I:22 , ASP I:24 , HIS I:25 , GLU I:28 , HIS I:29 , ARG I:148 , LYS I:177 , LYS I:179 , SER I:202 , GLY I:203 , GLY I:204 , ALA I:229 , VAL I:230 , GLY I:231 , ARG I:232 , HOH I:2073 , HOH I:2131 , HOH I:2133
BINDING SITE FOR RESIDUE FBP I 270
10
BC1
SOFTWARE
ALA J:22 , ASP J:24 , HIS J:25 , GLU J:28 , HIS J:29 , ARG J:148 , LYS J:177 , LYS J:179 , SER J:202 , GLY J:203 , GLY J:204 , ALA J:229 , VAL J:230 , GLY J:231 , ARG J:232 , HOH J:2135 , HOH J:2158 , HOH J:2159
BINDING SITE FOR RESIDUE FBP J 270
[
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
(2, 10)
Info
All SCOP Domains
1a: SCOP_d1w8sa1 (A:3-252)
2a: SCOP_d1w8sb_ (B:)
2b: SCOP_d1w8sc_ (C:)
2c: SCOP_d1w8sd_ (D:)
2d: SCOP_d1w8se_ (E:)
2e: SCOP_d1w8sf_ (F:)
2f: SCOP_d1w8sg_ (G:)
2g: SCOP_d1w8sh_ (H:)
2h: SCOP_d1w8si_ (I:)
2i: SCOP_d1w8sj_ (J:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
Class I aldolase
(182)
Protein domain
:
Archaeal fructose 1,6-bisphosphate aldolase
(5)
Thermoproteus tenax [TaxId: 2271]
(5)
1a
d1w8sa1
A:3-252
Protein domain
:
automated matches
(54)
Thermoproteus tenax [TaxId: 2271]
(1)
2a
d1w8sb_
B:
2b
d1w8sc_
C:
2c
d1w8sd_
D:
2d
d1w8se_
E:
2e
d1w8sf_
F:
2f
d1w8sg_
G:
2g
d1w8sh_
H:
2h
d1w8si_
I:
2i
d1w8sj_
J:
[
close SCOP info
]
CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_1w8sE00 (E:3-254)
1b: CATH_1w8sA00 (A:3-252)
1c: CATH_1w8sB00 (B:3-252)
1d: CATH_1w8sC00 (C:3-252)
1e: CATH_1w8sD00 (D:3-252)
1f: CATH_1w8sF00 (F:3-252)
1g: CATH_1w8sG00 (G:3-252)
1h: CATH_1w8sH00 (H:3-252)
1i: CATH_1w8sI00 (I:3-252)
1j: CATH_1w8sJ00 (J:3-252)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Thermoproteus tenax. Organism_taxid: 2271.
(6)
1a
1w8sE00
E:3-254
1b
1w8sA00
A:3-252
1c
1w8sB00
B:3-252
1d
1w8sC00
C:3-252
1e
1w8sD00
D:3-252
1f
1w8sF00
F:3-252
1g
1w8sG00
G:3-252
1h
1w8sH00
H:3-252
1i
1w8sI00
I:3-252
1j
1w8sJ00
J:3-252
[
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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
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 (423 KB)
Header - Asym.Unit
Biol.Unit 1 (211 KB)
Header - Biol.Unit 1
Biol.Unit 2 (212 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
1W8S
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help