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1OB5
Biol. Unit 1
Info
Asym.Unit (314 KB)
Biol.Unit 1 (298 KB)
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(1)
Title
:
T. AQUATICUS ELONGATION FACTOR EF-TU COMPLEXED WITH THE ANTIBIOTIC ENACYLOXIN IIA, A GTP ANALOG, AND PHE-TRNA
Authors
:
C. Dahlberg, R. C. Nielsen, A. Parmeggiani, J. Nyborg, P. Nissen
Date
:
24 Jan 03 (Deposition) - 13 Oct 05 (Release) - 19 Aug 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Hydrolase, Gtpase, Translation Elongation Factor, Transfer Rna, Gtp-Binding, Nucleotide-Binding, Protein Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Parmeggiani, I. M. Krab, T. Watanabe, R. C. Nielsen, C. Dahlberg, J. Nyborg, P. Nissen
Enacyloxin Iia Pinpoints A Binding Pocket Of Elongation Factor Tu For Development Of Novel Antibiotics.
J. Biol. Chem. V. 281 2893 2006
[
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Hetero Components
(13, 48)
Info
All Hetero Components
01a: 6-HYDRO-1-METHYLADENOSINE-5'-MONOP... (1MAa)
01b: 6-HYDRO-1-METHYLADENOSINE-5'-MONOP... (1MAb)
01c: 6-HYDRO-1-METHYLADENOSINE-5'-MONOP... (1MAc)
02a: 2N-METHYLGUANOSINE-5'-MONOPHOSPHAT... (2MGa)
02b: 2N-METHYLGUANOSINE-5'-MONOPHOSPHAT... (2MGb)
02c: 2N-METHYLGUANOSINE-5'-MONOPHOSPHAT... (2MGc)
03a: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCa)
03b: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCb)
03c: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCc)
03d: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCd)
03e: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCe)
03f: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCf)
04a: 5-METHYLURIDINE 5'-MONOPHOSPHATE (5MUa)
04b: 5-METHYLURIDINE 5'-MONOPHOSPHATE (5MUb)
04c: 5-METHYLURIDINE 5'-MONOPHOSPHATE (5MUc)
05a: 7N-METHYL-8-HYDROGUANOSINE-5'-MONO... (7MGa)
05b: 7N-METHYL-8-HYDROGUANOSINE-5'-MONO... (7MGb)
05c: 7N-METHYL-8-HYDROGUANOSINE-5'-MONO... (7MGc)
06a: ENACYLOXIN IIA (ENXa)
06b: ENACYLOXIN IIA (ENXb)
06c: ENACYLOXIN IIA (ENXc)
07a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
07b: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPb)
07c: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPc)
08a: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ua)
08b: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ub)
08c: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uc)
08d: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ud)
08e: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ue)
08f: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uf)
09a: N2-DIMETHYLGUANOSINE-5'-MONOPHOSPH... (M2Ga)
09b: N2-DIMETHYLGUANOSINE-5'-MONOPHOSPH... (M2Gb)
09c: N2-DIMETHYLGUANOSINE-5'-MONOPHOSPH... (M2Gc)
10a: MAGNESIUM ION (MGa)
10b: MAGNESIUM ION (MGb)
10c: MAGNESIUM ION (MGc)
11a: O2'-METHYLYCYTIDINE-5'-MONOPHOSPHA... (OMCa)
11b: O2'-METHYLYCYTIDINE-5'-MONOPHOSPHA... (OMCb)
11c: O2'-METHYLYCYTIDINE-5'-MONOPHOSPHA... (OMCc)
12a: O2'-METHYLGUANOSINE-5'-MONOPHOSPHA... (OMGa)
12b: O2'-METHYLGUANOSINE-5'-MONOPHOSPHA... (OMGb)
12c: O2'-METHYLGUANOSINE-5'-MONOPHOSPHA... (OMGc)
13a: PHENYLALANINAL (PHAa)
13b: PHENYLALANINAL (PHAb)
13c: PHENYLALANINAL (PHAc)
14a: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUa)
14b: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUb)
14c: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUc)
14d: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUd)
14e: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUe)
14f: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUf)
15a: WYBUTOSINE (YGa)
15b: WYBUTOSINE (YGb)
15c: WYBUTOSINE (YGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1MA
3
Mod. Nucleotide
6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2
2MG
3
Mod. Nucleotide
2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
3
5MC
6
Mod. Nucleotide
5-METHYLCYTIDINE-5'-MONOPHOSPHATE
4
5MU
3
Mod. Nucleotide
5-METHYLURIDINE 5'-MONOPHOSPHATE
5
7MG
3
Mod. Nucleotide
7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
6
ENX
3
Ligand/Ion
ENACYLOXIN IIA
7
GNP
3
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
8
H2U
6
Mod. Nucleotide
5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
9
M2G
3
Mod. Nucleotide
N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
10
MG
-1
Ligand/Ion
MAGNESIUM ION
11
OMC
3
Mod. Nucleotide
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
12
OMG
3
Mod. Nucleotide
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
13
PHA
3
Mod. Amino Acid
PHENYLALANINAL
14
PSU
6
Mod. Nucleotide
PSEUDOURIDINE-5'-MONOPHOSPHATE
15
YG
-1
Mod. Residue
WYBUTOSINE
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:20 , ASP A:21 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , TYR A:47 , ILE A:61 , THR A:62 , GLY A:84 , HIS A:85 , ASN A:136 , LYS A:137 , ASP A:139 , MET A:140 , SER A:174 , ALA A:175 , LEU A:176 , MG A:1407
BINDING SITE FOR RESIDUE GNP A1406
2
AC2
SOFTWARE
LYS A:24 , THR A:25 , THR A:62 , ASP A:81 , CYS A:82 , GNP A:1406
BINDING SITE FOR RESIDUE MG A1407
3
AC3
SOFTWARE
ARG A:117 , LEU A:121 , ARG A:124 , GLN A:125 , VAL A:126 , GLY A:127 , TYR A:161 , LEU A:323 , LYS A:325 , GLU A:326 , GLU A:327 , GLY A:328 , TYR A:343 , ARG A:345 , PHE A:386 , ALA A:387 , ALA A:397
BINDING SITE FOR RESIDUE ENX A1408
4
AC4
SOFTWARE
VAL C:20 , ASP C:21 , GLY C:23 , LYS C:24 , THR C:25 , THR C:26 , TYR C:47 , ILE C:61 , THR C:62 , GLY C:84 , HIS C:85 , ASN C:136 , LYS C:137 , ASP C:139 , MET C:140 , SER C:174 , ALA C:175 , LEU C:176 , MG C:1407
BINDING SITE FOR RESIDUE GNP C1406
5
AC5
SOFTWARE
LYS C:24 , THR C:25 , THR C:62 , ASP C:81 , CYS C:82 , GNP C:1406
BINDING SITE FOR RESIDUE MG C1407
6
AC6
SOFTWARE
ARG C:117 , LEU C:121 , ARG C:124 , GLN C:125 , VAL C:126 , GLY C:127 , TYR C:161 , LEU C:323 , LYS C:325 , GLU C:326 , GLU C:327 , GLY C:328 , TYR C:343 , ARG C:345 , PHE C:386 , ALA C:387 , ALA C:397
BINDING SITE FOR RESIDUE ENX C1408
7
AC7
SOFTWARE
VAL E:20 , ASP E:21 , GLY E:23 , LYS E:24 , THR E:25 , THR E:26 , TYR E:47 , ILE E:61 , THR E:62 , GLY E:84 , HIS E:85 , ASN E:136 , LYS E:137 , ASP E:139 , MET E:140 , SER E:174 , ALA E:175 , LEU E:176 , MG E:1407
BINDING SITE FOR RESIDUE GNP E1406
8
AC8
SOFTWARE
LYS E:24 , THR E:25 , THR E:62 , ASP E:81 , CYS E:82 , GNP E:1406
BINDING SITE FOR RESIDUE MG E1407
9
AC9
SOFTWARE
ARG E:117 , LEU E:121 , ARG E:124 , GLN E:125 , VAL E:126 , GLY E:127 , TYR E:161 , LEU E:323 , LYS E:325 , GLU E:326 , GLU E:327 , GLY E:328 , TYR E:343 , ARG E:345 , PHE E:386 , ALA E:387 , ALA E:397
BINDING SITE FOR RESIDUE ENX E1408
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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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:51-66,C:51-66,E:51-66)
;
View:
Select:
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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.
EFTU_THEAQ
52-67
3
A:51-66
C:51-66
E:51-66
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(3, 9)
Info
All SCOP Domains
1a: SCOP_d1ob5a2 (A:313-405)
1b: SCOP_d1ob5c2 (C:313-405)
1c: SCOP_d1ob5e2 (E:313-405)
2a: SCOP_d1ob5a1 (A:213-312)
2b: SCOP_d1ob5c1 (C:213-312)
2c: SCOP_d1ob5e1 (E:213-312)
3a: SCOP_d1ob5a3 (A:6-212)
3b: SCOP_d1ob5c3 (C:6-212)
3c: SCOP_d1ob5e3 (E:6-212)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Elongation factor/aminomethyltransferase common domain
(82)
Superfamily
:
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
(67)
Family
:
automated matches
(19)
Protein domain
:
automated matches
(19)
Thermus aquaticus [TaxId: 271]
(1)
1a
d1ob5a2
A:313-405
1b
d1ob5c2
C:313-405
1c
d1ob5e2
E:313-405
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Translation proteins
(218)
Family
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Thermus aquaticus [TaxId: 271]
(1)
2a
d1ob5a1
A:213-312
2b
d1ob5c1
C:213-312
2c
d1ob5e1
E:213-312
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)
Thermus aquaticus [TaxId: 271]
(1)
3a
d1ob5a3
A:6-212
3b
d1ob5c3
C:6-212
3c
d1ob5e3
E:6-212
[
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]
CATH Domains
(2, 9)
Info
all CATH domains
1a: CATH_1ob5A01 (A:6-213)
1b: CATH_1ob5C01 (C:6-213)
1c: CATH_1ob5E01 (E:6-213)
2a: CATH_1ob5A03 (A:311-404)
2b: CATH_1ob5C03 (C:311-404)
2c: CATH_1ob5E03 (E:311-404)
2d: CATH_1ob5A02 (A:216-307)
2e: CATH_1ob5C02 (C:216-307)
2f: CATH_1ob5E02 (E:216-307)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Thermus aquaticus. Organism_taxid: 271.
(14)
1a
1ob5A01
A:6-213
1b
1ob5C01
C:6-213
1c
1ob5E01
E:6-213
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Translation factors
(223)
Thermus aquaticus. Organism_taxid: 271.
(1)
2a
1ob5A03
A:311-404
2b
1ob5C03
C:311-404
2c
1ob5E03
E:311-404
2d
1ob5A02
A:216-307
2e
1ob5C02
C:216-307
2f
1ob5E02
E:216-307
[
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]
Pfam Domains
(3, 9)
Info
all PFAM domains
1a: PFAM_GTP_EFTU_1ob5E01 (E:9-212)
1b: PFAM_GTP_EFTU_1ob5E02 (E:9-212)
1c: PFAM_GTP_EFTU_1ob5E03 (E:9-212)
2a: PFAM_GTP_EFTU_D2_1ob5E04 (E:235-305)
2b: PFAM_GTP_EFTU_D2_1ob5E05 (E:235-305)
2c: PFAM_GTP_EFTU_D2_1ob5E06 (E:235-305)
3a: PFAM_GTP_EFTU_D3_1ob5E07 (E:309-404)
3b: PFAM_GTP_EFTU_D3_1ob5E08 (E:309-404)
3c: PFAM_GTP_EFTU_D3_1ob5E09 (E:309-404)
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Clans
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)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
GTP_EFTU
(39)
Thermus aquaticus
(3)
1a
GTP_EFTU-1ob5E01
E:9-212
1b
GTP_EFTU-1ob5E02
E:9-212
1c
GTP_EFTU-1ob5E03
E:9-212
Clan
:
no clan defined [family: GTP_EFTU_D2]
(39)
Family
:
GTP_EFTU_D2
(39)
Thermus aquaticus
(3)
2a
GTP_EFTU_D2-1ob5E04
E:235-305
2b
GTP_EFTU_D2-1ob5E05
E:235-305
2c
GTP_EFTU_D2-1ob5E06
E:235-305
Clan
:
no clan defined [family: GTP_EFTU_D3]
(11)
Family
:
GTP_EFTU_D3
(11)
Thermus aquaticus
(3)
3a
GTP_EFTU_D3-1ob5E07
E:309-404
3b
GTP_EFTU_D3-1ob5E08
E:309-404
3c
GTP_EFTU_D3-1ob5E09
E:309-404
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