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2IY5
Asym. Unit
Info
Asym.Unit (217 KB)
Biol.Unit 1 (417 KB)
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(1)
Title
:
PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH TRNA AND A PHENYLALANYL-ADENYLATE ANALOG
Authors
:
N. Moor, O. Kotik-Kogan, D. Tworowski, M. Sukhanova, M. Safro
Date
:
12 Jul 06 (Deposition) - 06 Sep 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,T
Biol. Unit 1: A,B,T (2x)
Keywords
:
Class Ii Aminoacyl-Trna Synthetase, Ligase, Rbd Domin, Magnesium, Sh3 Domain, Phenylalanyl-Trna Synthetase, Thermus Thermophilus, Protein Biosynthesis, Metal-Binding, Nucleotide-Binding, Rna-Binding, Atp-Binding, Trna-Binding, Helix-Turn-Helix Motif, Aminoacyl-Trna Synthetase
(Keyword Search:
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Reference
:
N. Moor, O. Kotik-Kogan, D. Tworowski, M. Sukhanova, M. Safro
The Crystal Structure Of The Ternary Complex Of Phenylalanyl-Trna Synthetase With Trna(Phe) And A Phenylalanyl-Adenylate Analogue Reveals A Conformational Switch Of The Cca End.
Biochemistry V. 45 10572 2006
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: ADENOSINE-5'-[PHENYLALANINOL-PHOSP... (FYAa)
2a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FYA
1
Ligand/Ion
ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE]
2
MG
1
Ligand/Ion
MAGNESIUM ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:452 , ASP B:458 , GLU B:461
BINDING SITE FOR RESIDUE MG B1781
2
AC2
SOFTWARE
MET A:148 , HIS A:178 , SER A:180 , GLN A:183 , ARG A:204 , GLU A:206 , GLU A:213 , PHE A:216 , GLN A:218 , GLU A:220 , PHE A:258 , VAL A:261 , LEU A:280 , GLY A:281 , GLY A:282 , ALA A:283 , ALA A:314 , PHE A:315 , GLY A:316 , GLY A:318 , ARG A:321 , ILE A:332 , A T:76
BINDING SITE FOR RESIDUE FYA A1351
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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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRBD (B:39-147)
2: B5 (B:399-474)
3: FDX_ACB (B:688-780)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRBD
PS50886
tRNA-binding domain profile.
SYFB_THETH
39-147
1
B:39-147
2
B5
PS51483
B5 domain profile.
SYFB_THETH
399-474
1
B:399-474
3
FDX_ACB
PS51447
Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.
SYFB_THETH
688-780
1
B:688-780
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(7, 8)
Info
All SCOP Domains
1a: SCOP_d2iy5a1 (A:15-84)
2a: SCOP_d2iy5b1 (B:1-38,B:152-190)
2b: SCOP_d2iy5b2 (B:400-474)
3a: SCOP_d2iy5b3 (B:39-151)
4a: SCOP_d2iy5b4 (B:191-399)
5a: SCOP_d2iy5a2 (A:85-350)
6a: SCOP_d2iy5b6 (B:475-681)
7a: SCOP_d2iy5b5 (B:682-781)
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(
)
(
)
Folds
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Long alpha-hairpin
(315)
Superfamily
:
tRNA-binding arm
(11)
Family
:
Phenylalanyl-tRNA synthetase (PheRS)
(2)
Protein domain
:
Phenylalanyl-tRNA synthetase (PheRS)
(2)
Thermus thermophilus [TaxId: 274]
(2)
1a
d2iy5a1
A:15-84
Fold
:
Putative DNA-binding domain
(45)
Superfamily
:
Putative DNA-binding domain
(45)
Family
:
Domains B1 and B5 of PheRS-beta, PheT
(11)
Protein domain
:
Domains B1 and B5 of PheRS-beta, PheT
(11)
Thermus thermophilus [TaxId: 274]
(11)
2a
d2iy5b1
B:1-38,B:152-190
2b
d2iy5b2
B:400-474
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Myf domain
(20)
Protein domain
:
Domain B2 of PheRS-beta, PheT
(11)
Thermus thermophilus [TaxId: 274]
(11)
3a
d2iy5b3
B:39-151
Fold
:
PheT/TilS domain
(12)
Superfamily
:
PheT/TilS domain
(12)
Family
:
B3/B4 domain of PheRS, PheT
(11)
Protein domain
:
B3/B4 domain of PheRS, PheT
(11)
Thermus thermophilus [TaxId: 274]
(11)
4a
d2iy5b4
B:191-399
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Class II aaRS and biotin synthetases
(165)
Superfamily
:
Class II aaRS and biotin synthetases
(165)
Family
:
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
(103)
Protein domain
:
Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS
(11)
Thermus thermophilus [TaxId: 274]
(11)
5a
d2iy5a2
A:85-350
Protein domain
:
Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain
(11)
Thermus thermophilus [TaxId: 274]
(11)
6a
d2iy5b6
B:475-681
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Anticodon-binding domain of PheRS
(11)
Family
:
Anticodon-binding domain of PheRS
(11)
Protein domain
:
Phenylalanyl-tRNA synthetase
(11)
Thermus thermophilus [TaxId: 274]
(11)
7a
d2iy5b5
B:682-781
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CATH Domains
(6, 7)
Info
all CATH domains
1a: CATH_2iy5B06 (B:690-781)
2a: CATH_2iy5B05 (B:489-679)
2b: CATH_2iy5A00 (A:15-350)
3a: CATH_2iy5B01 (B:1-37,B:154-186)
4a: CATH_2iy5B04 (B:401-474)
5a: CATH_2iy5B03 (B:187-400)
6a: CATH_2iy5B02 (B:38-153)
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)
Homologous Superfamilies
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.380, no name defined]
(12)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(1)
1a
2iy5B06
B:690-781
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(1)
2a
2iy5B05
B:489-679
2b
2iy5A00
A:15-350
Topology
:
Phenylalanyl-tRNA Synthetase; Chain B, domain 1
(22)
Homologous Superfamily
:
[code=3.30.56.10, no name defined]
(12)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(1)
3a
2iy5B01
B:1-37,B:154-186
Homologous Superfamily
:
[code=3.30.56.20, no name defined]
(12)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(1)
4a
2iy5B04
B:401-474
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
Phenylalanyl-tRNA Synthetase; Chain B, domain 3
(12)
Homologous Superfamily
:
Phenylalanyl-trna Synthetase, Chain B, domain 3
(12)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(1)
5a
2iy5B03
B:187-400
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(1)
6a
2iy5B02
B:38-153
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Pfam Domains
(0, 0)
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all PFAM domains
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