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.
1RV8
Asym. Unit
Info
Asym.Unit (213 KB)
Biol.Unit 1 (106 KB)
Biol.Unit 2 (106 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM THERMUS AQUATICUS IN COMPLEX WITH COBALT
Authors
:
T. Izard, J. Sygusch
Date
:
12 Dec 03 (Deposition) - 27 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Class Ii Aldolase, Metal-Depdendent Aldolase, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Izard, J. Sygusch
Induced Fit Movements And Metal Cofactor Selectivity Of Class Ii Aldolases: Structure Of Thermus Aquaticus Fructose-1, 6-Bisphosphate Aldolase.
J. Biol. Chem. V. 279 11825 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 21)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
1e: COBALT (II) ION (COe)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
5
Ligand/Ion
COBALT (II) ION
2
NA
4
Ligand/Ion
SODIUM ION
3
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:278 , SER B:49 , GLY B:51 , ARG B:257 , HOH B:1742 , HOH B:1866
BINDING SITE FOR RESIDUE SO4 B 1601
02
AC2
SOFTWARE
SER B:211 , ASN B:251 , ASP B:253 , THR B:254 , HOH B:1763 , HOH B:1827 , HOH B:1916
BINDING SITE FOR RESIDUE SO4 B 1602
03
AC3
SOFTWARE
SER A:49 , GLY A:51 , HOH A:1770 , HOH A:1883 , HOH A:1885 , ARG B:278
BINDING SITE FOR RESIDUE SO4 A 1603
04
AC4
SOFTWARE
HIS A:178 , GLY A:179 , LYS A:182 , GLY A:209 , ALA A:210 , SER A:211 , ASP A:253 , THR A:254 , HOH A:1753 , HOH A:1868
BINDING SITE FOR RESIDUE SO4 A 1604
05
AC5
SOFTWARE
ARG C:278 , SER D:49 , GLY D:51 , ARG D:257
BINDING SITE FOR RESIDUE SO4 D 1605
06
AC6
SOFTWARE
GLY D:209 , SER D:211 , ASN D:251 , ASP D:253 , THR D:254 , HOH D:1747 , HOH D:1844 , HOH D:1947
BINDING SITE FOR RESIDUE SO4 D 1606
07
AC7
SOFTWARE
SER C:49 , ARG C:257 , HOH C:1751 , ARG D:278 , HOH D:1859
BINDING SITE FOR RESIDUE SO4 D 1607
08
AC8
SOFTWARE
GLY C:209 , ALA C:210 , SER C:211 , ASN C:251 , ASP C:253 , THR C:254 , HOH C:1777
BINDING SITE FOR RESIDUE SO4 C 1608
09
AC9
SOFTWARE
ARG C:116 , HIS C:123 , HOH C:1754 , HOH C:1761
BINDING SITE FOR RESIDUE SO4 C 1609
10
BC1
SOFTWARE
ARG B:116 , HIS B:123 , GLY B:166 , HOH B:1788 , HOH B:1851
BINDING SITE FOR RESIDUE SO4 B 1610
11
BC2
SOFTWARE
ARG D:116 , HIS D:123 , HOH D:1881
BINDING SITE FOR RESIDUE SO4 D 1611
12
BC3
SOFTWARE
ARG A:116 , VAL A:119 , HIS A:123
BINDING SITE FOR RESIDUE SO4 A 1612
13
BC4
SOFTWARE
HIS B:81 , GLU B:132 , HIS B:178 , HIS B:208 , HOH B:1750
BINDING SITE FOR RESIDUE CO B 1701
14
BC5
SOFTWARE
HIS B:78 , ASP B:80 , GLU B:130 , LYS B:249 , ASN B:251
BINDING SITE FOR RESIDUE NA B 1702
15
BC6
SOFTWARE
HIS A:81 , HIS A:178 , HIS A:208 , CO A:1709 , HOH A:1918
BINDING SITE FOR RESIDUE CO A 1703
16
BC7
SOFTWARE
HIS A:78 , ASP A:80 , MET A:100 , GLU A:130 , HIS A:208 , LYS A:249 , ASN A:251 , HOH A:1712
BINDING SITE FOR RESIDUE NA A 1704
17
BC8
SOFTWARE
HIS D:81 , GLU D:132 , HIS D:178 , HIS D:208 , HOH D:1751
BINDING SITE FOR RESIDUE CO D 1705
18
BC9
SOFTWARE
HIS D:78 , ASP D:80 , GLU D:130 , HIS D:208 , LYS D:249 , ASN D:251 , HOH D:1716
BINDING SITE FOR RESIDUE NA D 1706
19
CC1
SOFTWARE
HIS C:81 , GLU C:132 , HIS C:178 , HIS C:208 , HOH C:1729
BINDING SITE FOR RESIDUE CO C 1707
20
CC2
SOFTWARE
HIS C:78 , ASP C:80 , GLU C:130 , HIS C:208 , LYS C:249 , ASN C:251 , HOH C:1709
BINDING SITE FOR RESIDUE NA C 1708
21
CC3
SOFTWARE
HIS A:81 , GLU A:132 , LEU A:136 , HIS A:178 , HIS A:208 , CO A:1703 , HOH A:1937
BINDING SITE FOR RESIDUE CO A 1709
[
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_d1rv8a_ (A:)
1b: SCOP_d1rv8b_ (B:)
1c: SCOP_d1rv8c_ (C:)
1d: SCOP_d1rv8d_ (D:)
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 II FBP aldolase
(9)
Protein domain
:
Fructose-bisphosphate aldolase (FBP aldolase)
(6)
Thermus aquaticus [TaxId: 271]
(2)
1a
d1rv8a_
A:
1b
d1rv8b_
B:
1c
d1rv8c_
C:
1d
d1rv8d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1rv8A00 (A:1-305)
1b: CATH_1rv8B00 (B:1-305)
1c: CATH_1rv8C00 (C:1-305)
1d: CATH_1rv8D00 (D:1-305)
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)
Thermus aquaticus. Organism_taxid: 271.
(2)
1a
1rv8A00
A:1-305
1b
1rv8B00
B:1-305
1c
1rv8C00
C:1-305
1d
1rv8D00
D:1-305
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_F_bP_aldolase_1rv8D01 (D:1-305)
1b: PFAM_F_bP_aldolase_1rv8D02 (D:1-305)
1c: PFAM_F_bP_aldolase_1rv8D03 (D:1-305)
1d: PFAM_F_bP_aldolase_1rv8D04 (D:1-305)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
F_bP_aldolase
(7)
Thermus aquaticus
(1)
1a
F_bP_aldolase-1rv8D01
D:1-305
1b
F_bP_aldolase-1rv8D02
D:1-305
1c
F_bP_aldolase-1rv8D03
D:1-305
1d
F_bP_aldolase-1rv8D04
D:1-305
[
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 (213 KB)
Header - Asym.Unit
Biol.Unit 1 (106 KB)
Header - Biol.Unit 1
Biol.Unit 2 (106 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
1RV8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help