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1FYF
Asym. Unit
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Asym.Unit (147 KB)
Biol.Unit 1 (142 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL ADENYLATE ANALOG
Authors
:
R. Sankaranarayanan, A. C. Dock-Bregeon, D. Moras
Date
:
29 Sep 00 (Deposition) - 27 Dec 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Amino Acid Recognition, Zinc Ion, Trna-Synthetase, Adenylate Analog, Deletion Mutant, Ligase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Dock-Bregeon, R. Sankaranarayanan, P. Romby, J. Caillet, M. Springer, B. Rees, C. S. Francklyn, C. Ehresmann, D. Moras
Transfer Rna-Mediated Editing In Threonyl-Trna Synthetase. The Class Ii Solution To The Double Discrimination Problem.
Cell(Cambridge, Mass. ) V. 103 877 2000
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOS... (SSAa)
1b: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOS... (SSAb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
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No.
Name
Count
Type
Full Name
1
SSA
2
Ligand/Ion
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
2
ZN
2
Ligand/Ion
ZINC ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:334 , HIS A:385 , HIS A:511 , SSA A:1001
BINDING SITE FOR RESIDUE ZN A 650
2
AC2
SOFTWARE
CYS B:334 , HIS B:385 , HIS B:511 , SSA B:2001
BINDING SITE FOR RESIDUE ZN B 650
3
AC3
SOFTWARE
MET A:332 , CYS A:334 , ARG A:363 , GLU A:365 , MET A:374 , ARG A:375 , VAL A:376 , PHE A:379 , GLN A:381 , ASP A:383 , HIS A:385 , TYR A:462 , GLN A:479 , CYS A:480 , GLN A:484 , HIS A:511 , GLY A:516 , SER A:517 , ARG A:520 , ZN A:650 , HOH A:1012 , HOH A:1071
BINDING SITE FOR RESIDUE SSA A 1001
4
AC4
SOFTWARE
MET B:332 , CYS B:334 , ARG B:363 , GLU B:365 , MET B:374 , ARG B:375 , VAL B:376 , PHE B:379 , GLN B:381 , ASP B:383 , HIS B:385 , TYR B:462 , GLN B:479 , CYS B:480 , GLN B:484 , HIS B:511 , GLY B:516 , SER B:517 , ARG B:520 , ZN B:650 , HOH B:2006 , HOH B:2066
BINDING SITE FOR RESIDUE SSA B 2001
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1fyfa2 (A:242-532)
1b: SCOP_d1fyfb2 (B:242-532)
2a: SCOP_d1fyfa1 (A:533-642)
2b: SCOP_d1fyfb1 (B:533-642)
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Protein Domains
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(
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Organisms
(
)
(
)
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
:
Threonyl-tRNA synthetase (ThrRS)
(7)
Escherichia coli [TaxId: 562]
(5)
1a
d1fyfa2
A:242-532
1b
d1fyfb2
B:242-532
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Anticodon-binding domain-like
(97)
Superfamily
:
Class II aaRS ABD-related
(40)
Family
:
Anticodon-binding domain of Class II aaRS
(33)
Protein domain
:
Threonyl-tRNA synthetase (ThrRS), C-terminal domain
(7)
Escherichia coli [TaxId: 562]
(5)
2a
d1fyfa1
A:533-642
2b
d1fyfb1
B:533-642
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1fyfA01 (A:242-530)
1b: CATH_1fyfB01 (B:242-530)
2a: CATH_1fyfA02 (A:531-642)
2b: CATH_1fyfB02 (B:531-642)
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Organisms
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(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Escherichia coli. Organism_taxid: 562.
(7)
1a
1fyfA01
A:242-530
1b
1fyfB01
B:242-530
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.800, no name defined]
(40)
Escherichia coli. Organism_taxid: 562.
(3)
2a
1fyfA02
A:531-642
2b
1fyfB02
B:531-642
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (147 KB)
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