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.
1FZW
Biol. Unit 1
Info
Asym.Unit (862 KB)
Biol.Unit 1 (430 KB)
Biol.Unit 2 (432 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). APO ENZYME.
Authors
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
Date
:
04 Oct 00 (Deposition) - 27 Dec 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Rhamnose, Nucleotidyltransferase, Pyrophosphorylase, Thymidylyltransferase, Allostery
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
The Structural Basis Of The Catalytic Mechanism And Regulation Of Glucose-1-Phosphate Thymidylyltransferase (Rmla).
Embo J. V. 19 6652 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 10)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
1l: SULFATE ION (SO4l)
1m: SULFATE ION (SO4m)
1n: SULFATE ION (SO4n)
1o: SULFATE ION (SO4o)
1p: SULFATE ION (SO4p)
1q: SULFATE ION (SO4q)
1r: SULFATE ION (SO4r)
1s: SULFATE ION (SO4s)
1t: SULFATE ION (SO4t)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
10
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC7 (SOFTWARE)
11: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:116 , ASP A:117 , GLY C:218 , ARG C:219 , GLY C:220 , HOH C:5007 , HOH C:5064 , HOH C:5229 , HOH C:5240
BINDING SITE FOR RESIDUE SO4 C 3600
02
AC2
SOFTWARE
HIS B:116 , ASP B:117 , HOH B:3735 , HOH B:3800 , GLY D:218 , ARG D:219 , GLY D:220 , HOH D:3923 , HOH D:3941
BINDING SITE FOR RESIDUE SO4 D 3601
03
AC3
SOFTWARE
GLY A:218 , ARG A:219 , GLY A:220 , HOH A:3723 , HOH A:3761 , HOH A:3839 , HIS C:116 , ASP C:117 , HOH C:5022 , HOH C:5197
BINDING SITE FOR RESIDUE SO4 A 3602
04
AC4
SOFTWARE
GLY B:218 , ARG B:219 , GLY B:220 , HOH B:3765 , HOH B:3771 , HOH B:3792 , HIS D:116 , ASP D:117 , HOH D:3806 , HOH D:3895 , HOH D:4030
BINDING SITE FOR RESIDUE SO4 B 3603
05
AC9
SOFTWARE
ARG A:128 , GLU A:215 , HOH A:3801 , ASP F:151 , GLN F:152 , HOH F:4877 , HOH F:4938
BINDING SITE FOR RESIDUE SO4 A 3700
06
BC1
SOFTWARE
ARG B:128 , GLU B:215 , HOH B:3986 , HOH B:4011 , ASP E:151 , GLN E:152
BINDING SITE FOR RESIDUE SO4 B 3701
07
BC2
SOFTWARE
ARG C:128 , GLN C:129 , THR C:130
BINDING SITE FOR RESIDUE SO4 C 3702
08
BC3
SOFTWARE
GLN D:129 , THR D:130
BINDING SITE FOR RESIDUE SO4 D 3703
09
BC4
SOFTWARE
ASP D:151 , GLN D:152 , ARG H:128 , GLU H:215 , HOH H:6192 , HOH H:6269
BINDING SITE FOR RESIDUE SO4 D 3800
10
BC7
SOFTWARE
ASP C:151 , GLN C:152 , ARG G:128 , GLU G:215 , HOH G:5068 , HOH G:5204
BINDING SITE FOR RESIDUE SO4 G 3704
11
BC8
SOFTWARE
ARG C:62 , ARG D:62
BINDING SITE FOR RESIDUE SO4 C 5000
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1fzwa_ (A:)
1b: SCOP_d1fzwb_ (B:)
1c: SCOP_d1fzwc_ (C:)
1d: SCOP_d1fzwd_ (D:)
1e: SCOP_d1fzwe_ (E:)
1f: SCOP_d1fzwf_ (F:)
1g: SCOP_d1fzwg_ (G:)
1h: SCOP_d1fzwh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
glucose-1-phosphate thymidylyltransferase
(43)
Protein domain
:
RmlA (RfbA)
(27)
Pseudomonas aeruginosa [TaxId: 287]
(9)
1a
d1fzwa_
A:
1b
d1fzwb_
B:
1c
d1fzwc_
C:
1d
d1fzwd_
D:
1e
d1fzwe_
E:
1f
d1fzwf_
F:
1g
d1fzwg_
G:
1h
d1fzwh_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1fzwA00 (A:2-293)
1b: CATH_1fzwB00 (B:2-293)
1c: CATH_1fzwD00 (D:2-293)
1d: CATH_1fzwE00 (E:2-293)
1e: CATH_1fzwG00 (G:2-293)
1f: CATH_1fzwH00 (H:2-293)
1g: CATH_1fzwC00 (C:1-293)
1h: CATH_1fzwF00 (F:1-293)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Pseudomonas aeruginosa. Organism_taxid: 287.
(7)
1a
1fzwA00
A:2-293
1b
1fzwB00
B:2-293
1c
1fzwD00
D:2-293
1d
1fzwE00
E:2-293
1e
1fzwG00
G:2-293
1f
1fzwH00
H:2-293
1g
1fzwC00
C:1-293
1h
1fzwF00
F:1-293
[
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 (862 KB)
Header - Asym.Unit
Biol.Unit 1 (430 KB)
Header - Biol.Unit 1
Biol.Unit 2 (432 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
1FZW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help