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1ZM9
Asym. Unit
Info
Asym.Unit (493 KB)
Biol.Unit 1 (168 KB)
Biol.Unit 2 (168 KB)
Biol.Unit 3 (167 KB)
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(1)
Title
:
STRUCTURE OF EEF2-ETA IN COMPLEX WITH PJ34
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
:
2.80
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
)
[
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: {3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H... (DDEa)
1b: {3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H... (DDEb)
1c: {3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H... (DDEc)
2a: N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6... (P34a)
2b: N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6... (P34b)
2c: N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6... (P34c)
View:
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Label:
No.
Name
Count
Type
Full Name
1
DDE
3
Mod. Amino Acid
{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM
2
P34
3
Ligand/Ion
N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS B:440 , GLY B:441 , TYR B:470 , ILE B:471 , ALA B:478 , TYR B:481
BINDING SITE FOR RESIDUE P34 B 700
2
AC2
SOFTWARE
HIS D:440 , GLY D:441 , TYR D:470 , ALA D:478 , TYR D:481
BINDING SITE FOR RESIDUE P34 D 701
3
AC3
SOFTWARE
HIS F:440 , GLY F:441 , TYR F:470 , ILE F:471 , ALA F:478 , TYR F:481 , GLU F:553
BINDING SITE FOR RESIDUE P34 F 702
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: G_TR_1 (A:67-73,C:67-73,E: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
3
A:67-73
C:67-73
E:67-73
[
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Exons
(1, 3)
Info
All Exons
Exon 1.2 (A:2-842 (gaps) | C:2-842 (gaps) | ...)
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All Exon Boundaries
1: Boundary -/1.2
2: Boundary 1.2/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.2
YOR133W
2
YOR133W.1
XV:575099-577627
2529
EF2_YEAST
1-842
842
3
A:2-842 (gaps)
C:2-842 (gaps)
E:2-842 (gaps)
841
841
841
[
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SCOP Domains
(5, 18)
Info
All SCOP Domains
1a: SCOP_d1zm9a1 (A:344-481)
1b: SCOP_d1zm9c1 (C:344-481)
1c: SCOP_d1zm9e1 (E:344-481)
2a: SCOP_d1zm9b_ (B:)
2b: SCOP_d1zm9d_ (D:)
2c: SCOP_d1zm9f_ (F:)
3a: SCOP_d1zm9a4 (A:482-560)
3b: SCOP_d1zm9a5 (A:726-842)
3c: SCOP_d1zm9c4 (C:482-560)
3d: SCOP_d1zm9c5 (C:726-842)
3e: SCOP_d1zm9e4 (E:482-560)
3f: SCOP_d1zm9e5 (E:726-842)
4a: SCOP_d1zm9a3 (A:561-725)
4b: SCOP_d1zm9c3 (C:561-725)
4c: SCOP_d1zm9e3 (E:561-725)
5a: SCOP_d1zm9a2 (A:2-343)
5b: SCOP_d1zm9c2 (C:2-343)
5c: SCOP_d1zm9e2 (E:2-343)
View:
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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
:
Elongation factors
(77)
Protein domain
:
Elongation factor 2 (eEF-2), domain II
(13)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(13)
1a
d1zm9a1
A:344-481
1b
d1zm9c1
C:344-481
1c
d1zm9e1
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
:
automated matches
(21)
Pseudomonas aeruginosa [TaxId: 287]
(4)
2a
d1zm9b_
B:
2b
d1zm9d_
D:
2c
d1zm9f_
F:
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
EF-G C-terminal domain-like
(33)
Family
:
EF-G/eEF-2 domains III and V
(24)
Protein domain
:
Elongation factor 2 (eEF-2)
(13)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(13)
3a
d1zm9a4
A:482-560
3b
d1zm9a5
A:726-842
3c
d1zm9c4
C:482-560
3d
d1zm9c5
C:726-842
3e
d1zm9e4
E:482-560
3f
d1zm9e5
E:726-842
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
Translational machinery components
(150)
Protein domain
:
Elongation factor 2 (eEF-2), domain IV
(13)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(13)
4a
d1zm9a3
A:561-725
4b
d1zm9c3
C:561-725
4c
d1zm9e3
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
:
Elongation factor 2 (eEF-2), N-terminal (G) domain
(13)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(13)
5a
d1zm9a2
A:2-343
5b
d1zm9c2
C:2-343
5c
d1zm9e2
E:2-343
[
close SCOP info
]
CATH Domains
(7, 21)
Info
all CATH domains
1a: CATH_1zm9A06 (A:722-842)
1b: CATH_1zm9C06 (C:722-842)
1c: CATH_1zm9E06 (E:722-842)
2a: CATH_1zm9A04 (A:482-562)
2b: CATH_1zm9C04 (C:482-562)
2c: CATH_1zm9E04 (E:482-562)
3a: CATH_1zm9A05 (A:568-721)
3b: CATH_1zm9C05 (C:568-721)
3c: CATH_1zm9E05 (E:568-721)
4a: CATH_1zm9A01 (A:2-221,A:329-344)
4b: CATH_1zm9C01 (C:2-221,C:329-344)
4c: CATH_1zm9E01 (E:2-222,E:329-344)
5a: CATH_1zm9B00 (B:399-605)
5b: CATH_1zm9D00 (D:399-605)
5c: CATH_1zm9F00 (F:399-605)
6a: CATH_1zm9A02 (A:222-328)
6b: CATH_1zm9C02 (C:222-328)
6c: CATH_1zm9E02 (E:223-328)
7a: CATH_1zm9A03 (A:345-481)
7b: CATH_1zm9C03 (C:345-481)
7c: CATH_1zm9E03 (E:345-481)
View:
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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
1zm9A06
A:722-842
1b
1zm9C06
C:722-842
1c
1zm9E06
E:722-842
Homologous Superfamily
:
Elongation Factor G (Translational Gtpase), domain 3
(20)
Baker's yeast (Saccharomyces cerevisiae)
(7)
2a
1zm9A04
A:482-562
2b
1zm9C04
C:482-562
2c
1zm9E04
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
1zm9A05
A:568-721
3b
1zm9C05
C:568-721
3c
1zm9E05
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
1zm9A01
A:2-221,A:329-344
4b
1zm9C01
C:2-221,C:329-344
4c
1zm9E01
E:2-222,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
1zm9B00
B:399-605
5b
1zm9D00
D:399-605
5c
1zm9F00
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
1zm9A02
A:222-328
6b
1zm9C02
C:222-328
6c
1zm9E02
E:223-328
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
1zm9A03
A:345-481
7b
1zm9C03
C:345-481
7c
1zm9E03
E:345-481
[
close CATH info
]
Pfam Domains
(5, 15)
Info
all PFAM domains
1a: PFAM_EFG_C_1zm9E01 (E:723-811)
1b: PFAM_EFG_C_1zm9E02 (E:723-811)
1c: PFAM_EFG_C_1zm9E03 (E:723-811)
2a: PFAM_GTP_EFTU_1zm9E04 (E:17-344)
2b: PFAM_GTP_EFTU_1zm9E05 (E:17-344)
2c: PFAM_GTP_EFTU_1zm9E06 (E:17-344)
3a: PFAM_EFG_IV_1zm9E07 (E:604-721)
3b: PFAM_EFG_IV_1zm9E08 (E:604-721)
3c: PFAM_EFG_IV_1zm9E09 (E:604-721)
4a: PFAM_Exotox_A_cataly_1zm9F01 (F:399-605)
4b: PFAM_Exotox_A_cataly_1zm9F02 (F:399-605)
4c: PFAM_Exotox_A_cataly_1zm9F03 (F:399-605)
5a: PFAM_GTP_EFTU_D2_1zm9E10 (E:393-470)
5b: PFAM_GTP_EFTU_D2_1zm9E11 (E:393-470)
5c: PFAM_GTP_EFTU_D2_1zm9E12 (E:393-470)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EF-G_C
(20)
Family
:
EFG_C
(14)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(9)
1a
EFG_C-1zm9E01
E:723-811
1b
EFG_C-1zm9E02
E:723-811
1c
EFG_C-1zm9E03
E:723-811
Clan
:
P-loop_NTPase
(1112)
Family
:
GTP_EFTU
(39)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(11)
2a
GTP_EFTU-1zm9E04
E:17-344
2b
GTP_EFTU-1zm9E05
E:17-344
2c
GTP_EFTU-1zm9E06
E:17-344
Clan
:
S5
(103)
Family
:
EFG_IV
(11)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(9)
3a
EFG_IV-1zm9E07
E:604-721
3b
EFG_IV-1zm9E08
E:604-721
3c
EFG_IV-1zm9E09
E:604-721
Clan
:
no clan defined [family: Exotox-A_cataly]
(4)
Family
:
Exotox-A_cataly
(4)
Pseudomonas aeruginosa
(4)
4a
Exotox-A_cataly-1zm9F01
F:399-605
4b
Exotox-A_cataly-1zm9F02
F:399-605
4c
Exotox-A_cataly-1zm9F03
F:399-605
Clan
:
no clan defined [family: GTP_EFTU_D2]
(39)
Family
:
GTP_EFTU_D2
(39)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(11)
5a
GTP_EFTU_D2-1zm9E10
E:393-470
5b
GTP_EFTU_D2-1zm9E11
E:393-470
5c
GTP_EFTU_D2-1zm9E12
E:393-470
[
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