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.
1ZM2
Biol. Unit 1
Info
Asym.Unit (493 KB)
Biol.Unit 1 (167 KB)
Biol.Unit 2 (167 KB)
Biol.Unit 3 (168 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF ADP-RIBOSYLATED EEF2 IN COMPLEX WITH CATALYTIC FRAGMENT OF ETA
Authors
:
R. Joergensen, A. R. Merrill, S. P. Yates, V. E. Marquez, A. L. Schwan, T. Boesen, G. R. Andersen
Date
:
10 May 05 (Deposition) - 24 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.07
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Elongation Factor, Toxin, Adp-Ribosylation, Biosynthetic Protein/Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Joergensen, A. R. Merrill, S. P. Yates, V. E. Marquez, A. L. Schwan, T. Boesen, G. R. Andersen
Exotoxin A-Eef2 Complex Structure Indicates Adp Ribosylation By Ribosome Mimicry.
Nature V. 436 979 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: ADENOSINE-5-DIPHOSPHORIBOSE (APRa)
2a: {3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H... (DDEa)
2b: {3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H... (DDEb)
2c: {3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H... (DDEc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
APR
-1
Ligand/Ion
ADENOSINE-5-DIPHOSPHORIBOSE
2
DDE
1
Mod. Amino Acid
{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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: G_TR_1 (A:67-73)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G_TR_1
PS00301
Translational (tr)-type guanine nucleotide-binding (G) domain signature.
EF2_YEAST
58-73
1
A:67-73
-
-
[
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
(5, 18)
Info
All SCOP Domains
1a: SCOP_d1zm2a1 (A:344-481)
1b: SCOP_d1zm2c1 (C:344-481)
1c: SCOP_d1zm2e1 (E:344-481)
2a: SCOP_d1zm2b_ (B:)
2b: SCOP_d1zm2d_ (D:)
2c: SCOP_d1zm2f_ (F:)
3a: SCOP_d1zm2a4 (A:482-560)
3b: SCOP_d1zm2c4 (C:482-560)
3c: SCOP_d1zm2c5 (C:726-842)
3d: SCOP_d1zm2e4 (E:482-560)
3e: SCOP_d1zm2e5 (E:726-842)
3f: SCOP_d1zm2a5 (A:726-842)
4a: SCOP_d1zm2a3 (A:561-725)
4b: SCOP_d1zm2c3 (C:561-725)
4c: SCOP_d1zm2e3 (E:561-725)
5a: SCOP_d1zm2a2 (A:2-343)
5b: SCOP_d1zm2c2 (C:2-343)
5c: SCOP_d1zm2e2 (E:2-343)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Translation proteins
(218)
Family
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(4)
1a
d1zm2a1
A:344-481
1b
d1zm2c1
C:344-481
1c
d1zm2e1
E:344-481
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ADP-ribosylation
(157)
Superfamily
:
ADP-ribosylation
(157)
Family
:
ADP-ribosylating toxins
(85)
Protein domain
:
Exotoxin A, C-terminal domain
(9)
Pseudomonas aeruginosa [TaxId: 287]
(9)
2a
d1zm2b_
B:
2b
d1zm2d_
D:
2c
d1zm2f_
F:
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
EF-G C-terminal domain-like
(33)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(4)
3a
d1zm2a4
A:482-560
3b
d1zm2c4
C:482-560
3c
d1zm2c5
C:726-842
3d
d1zm2e4
E:482-560
3e
d1zm2e5
E:726-842
3f
d1zm2a5
A:726-842
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
4a
d1zm2a3
A:561-725
4b
d1zm2c3
C:561-725
4c
d1zm2e3
E:561-725
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
automated matches
(173)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(9)
5a
d1zm2a2
A:2-343
5b
d1zm2c2
C:2-343
5c
d1zm2e2
E:2-343
[
close SCOP info
]
CATH Domains
(7, 21)
Info
all CATH domains
1a: CATH_1zm2A06 (A:722-842)
1b: CATH_1zm2C06 (C:722-842)
1c: CATH_1zm2E06 (E:722-842)
2a: CATH_1zm2A04 (A:482-562)
2b: CATH_1zm2C04 (C:482-562)
2c: CATH_1zm2E04 (E:482-562)
3a: CATH_1zm2A05 (A:568-721)
3b: CATH_1zm2C05 (C:568-721)
3c: CATH_1zm2E05 (E:568-721)
4a: CATH_1zm2A01 (A:2-221,A:329-344)
4b: CATH_1zm2C01 (C:2-221,C:329-344)
4c: CATH_1zm2E01 (E:2-221,E:329-344)
5a: CATH_1zm2B00 (B:399-605)
5b: CATH_1zm2D00 (D:399-605)
5c: CATH_1zm2F00 (F:399-605)
6a: CATH_1zm2A02 (A:222-328)
6b: CATH_1zm2C02 (C:222-328)
6c: CATH_1zm2E02 (E:222-328)
7a: CATH_1zm2A03 (A:345-481)
7b: CATH_1zm2C03 (C:345-481)
7c: CATH_1zm2E03 (E:345-481)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.240, no name defined]
(21)
Baker's yeast (Saccharomyces cerevisiae)
(7)
1a
1zm2A06
A:722-842
1b
1zm2C06
C:722-842
1c
1zm2E06
E:722-842
Homologous Superfamily
:
Elongation Factor G (Translational Gtpase), domain 3
(20)
Baker's yeast (Saccharomyces cerevisiae)
(7)
2a
1zm2A04
A:482-562
2b
1zm2C04
C:482-562
2c
1zm2E04
E:482-562
Topology
:
Ribosomal Protein S5; domain 2
(189)
Homologous Superfamily
:
[code=3.30.230.10, no name defined]
(170)
Baker's yeast (Saccharomyces cerevisiae)
(10)
3a
1zm2A05
A:568-721
3b
1zm2C05
C:568-721
3c
1zm2E05
E:568-721
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Baker's yeast (Saccharomyces cerevisiae)
(61)
4a
1zm2A01
A:2-221,A:329-344
4b
1zm2C01
C:2-221,C:329-344
4c
1zm2E01
E:2-221,E:329-344
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Diphtheria Toxin; domain 1
(22)
Homologous Superfamily
:
Diphtheria Toxin, domain 1
(22)
Baker's yeast (Saccharomyces cerevisiae)
(8)
5a
1zm2B00
B:399-605
5b
1zm2D00
D:399-605
5c
1zm2F00
F:399-605
Topology
:
Yeast translation eEF2 (G' domain)
(7)
Homologous Superfamily
:
Yeast translation eEF2 (G' domain)
(7)
Baker's yeast (Saccharomyces cerevisiae)
(7)
6a
1zm2A02
A:222-328
6b
1zm2C02
C:222-328
6c
1zm2E02
E:222-328
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Translation factors
(223)
Baker's yeast (Saccharomyces cerevisiae)
(13)
7a
1zm2A03
A:345-481
7b
1zm2C03
C:345-481
7c
1zm2E03
E:345-481
[
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
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 (493 KB)
Header - Asym.Unit
Biol.Unit 1 (167 KB)
Header - Biol.Unit 1
Biol.Unit 2 (167 KB)
Header - Biol.Unit 2
Biol.Unit 3 (168 KB)
Header - Biol.Unit 3
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
1ZM2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help