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1YFS
Asym. Unit
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Asym.Unit (158 KB)
Biol.Unit 1 (79 KB)
Biol.Unit 2 (79 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-ALANINE
Authors
:
M. A. Swairjo, P. R. Schimmel
Date
:
03 Jan 05 (Deposition) - 25 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.08
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Alpha-Beta Fold, Helix-Loop-Helix Motif, Amino Acid Binding, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. A. Swairjo, P. R. Schimmel
Breaking Sieve For Steric Exclusion Of A Noncognate Amino Acid From Active Site Of A Trna Synthetase.
Proc. Natl. Acad. Sci. Usa V. 102 988 2005
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: ALANINE (ALAa)
1b: ALANINE (ALAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALA
2
Mod. Amino Acid
ALANINE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:194 , ASP A:217 , THR A:218 , GLY A:219 , HOH A:1513 , HOH A:1600
BINDING SITE FOR RESIDUE ALA A 1500
2
AC2
SOFTWARE
MET B:92 , ASN B:194 , ASP B:217 , THR B:218 , GLY B:219 , HOH B:2501 , HOH B:2648
BINDING SITE FOR RESIDUE ALA B 2500
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: AA_TRNA_LIGASE_II_ALA (A:2-457,B:2-457)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRNA_LIGASE_II_ALA
PS50860
Alanyl-transfer RNA synthetases family profile.
SYA_AQUAE
3-704
2
A:2-457
B:2-457
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Exons
(0, 0)
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1yfsa1 (A:237-457)
1b: SCOP_d1yfsb1 (B:237-457)
2a: SCOP_d1yfsa2 (A:1-236)
2b: SCOP_d1yfsb2 (B:1-236)
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)
Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
(6)
Superfamily
:
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
(6)
Family
:
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
(6)
Protein domain
:
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
(6)
Aquifex aeolicus [TaxId: 63363]
(6)
1a
d1yfsa1
A:237-457
1b
d1yfsb1
B:237-457
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
:
Alanyl-tRNA synthetase (AlaRS)
(6)
Aquifex aeolicus [TaxId: 63363]
(6)
2a
d1yfsa2
A:1-236
2b
d1yfsb2
B:1-236
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1yfsA01 (A:1-233)
1b: CATH_1yfsB01 (B:1-233)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Aquifex aeolicus. Organism_taxid: 63363.
(6)
1a
1yfsA01
A:1-233
1b
1yfsB01
B:1-233
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_tRNA_synt_2c_1yfsB01 (B:6-453)
1b: PFAM_tRNA_synt_2c_1yfsB02 (B:6-453)
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Clans
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Clan
:
tRNA_synt_II
(64)
Family
:
tRNA-synt_2c
(8)
Aquifex aeolicus
(4)
1a
tRNA-synt_2c-1yfsB01
B:6-453
1b
tRNA-synt_2c-1yfsB02
B:6-453
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (158 KB)
Header - Asym.Unit
Biol.Unit 1 (79 KB)
Header - Biol.Unit 1
Biol.Unit 2 (79 KB)
Header - Biol.Unit 2
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