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.
1CDE
Biol. Unit 2
Info
Asym.Unit (141 KB)
Biol.Unit 1 (37 KB)
Biol.Unit 2 (37 KB)
Biol.Unit 3 (37 KB)
Biol.Unit 4 (37 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
Authors
:
R. J. Almassy, C. A. Janson, C. -C. Kan, Z. Hostomska
Date
:
15 May 92 (Deposition) - 31 Oct 93 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Transferase(Formyl)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. J. Almassy, C. A. Janson, C. C. Kan, Z. Hostomska
Structures Of Apo And Complexed Escherichia Coli Glycinamide Ribonucleotide Transformylase.
Proc. Natl. Acad. Sci. Usa V. 89 6114 1992
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: 5-DEAZAFOLIC ACID (DZFa)
1b: 5-DEAZAFOLIC ACID (DZFb)
1c: 5-DEAZAFOLIC ACID (DZFc)
1d: 5-DEAZAFOLIC ACID (DZFd)
2a: GLYCINAMIDE RIBONUCLEOTIDE (GARa)
2b: GLYCINAMIDE RIBONUCLEOTIDE (GARb)
2c: GLYCINAMIDE RIBONUCLEOTIDE (GARc)
2d: GLYCINAMIDE RIBONUCLEOTIDE (GARd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DZF
1
Ligand/Ion
5-DEAZAFOLIC ACID
2
GAR
1
Ligand/Ion
GLYCINAMIDE RIBONUCLEOTIDE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
ASN B:10 , GLY B:11 , SER B:12 , ASN B:13 , GLY B:87 , MET B:89 , ILE B:107 , HIS B:108 , PRO B:109 , GLN B:170 , GLU B:173 , DZF B:225
BINDING SITE FOR RESIDUE GAR B 222
2
AC4
SOFTWARE
MET B:89 , ARG B:90 , ILE B:91 , LEU B:92 , VAL B:97 , ASN B:106 , VAL B:139 , THR B:140 , ASP B:141 , GLU B:142 , ASP B:144 , GAR B:222
BINDING SITE FOR RESIDUE DZF B 225
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: GART (B:133-156)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GART
PS00373
Phosphoribosylglycinamide formyltransferase active site.
PUR3_ECOLI
133-156
1
-
B:133-156
-
-
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1cdea_ (A:)
1b: SCOP_d1cdeb_ (B:)
1c: SCOP_d1cdec_ (C:)
1d: SCOP_d1cded_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formyltransferase
(42)
Superfamily
:
Formyltransferase
(42)
Family
:
Formyltransferase
(34)
Protein domain
:
Glycinamide ribonucleotide transformylase, GART
(24)
Escherichia coli [TaxId: 562]
(9)
1a
d1cdea_
A:
1b
d1cdeb_
B:
1c
d1cdec_
C:
1d
d1cded_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1cdeA00 (A:1-209)
1b: CATH_1cdeB00 (B:1-209)
1c: CATH_1cdeC00 (C:1-209)
1d: CATH_1cdeD00 (D:1-209)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.170, no name defined]
(28)
Escherichia coli. Organism_taxid: 562.
(3)
1a
1cdeA00
A:1-209
1b
1cdeB00
B:1-209
1c
1cdeC00
C:1-209
1d
1cdeD00
D:1-209
[
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 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 (141 KB)
Header - Asym.Unit
Biol.Unit 1 (37 KB)
Header - Biol.Unit 1
Biol.Unit 2 (37 KB)
Header - Biol.Unit 2
Biol.Unit 3 (37 KB)
Header - Biol.Unit 3
Biol.Unit 4 (37 KB)
Header - Biol.Unit 4
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
1CDE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
