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1F7U
Asym. Unit
Info
Asym.Unit (151 KB)
Biol.Unit 1 (144 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNA(ARG) AND L-ARG
Authors
:
B. Delagoutte, D. Moras, J. Cavarelli
Date
:
28 Jun 00 (Deposition) - 27 Jun 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rna-Protein Complex, Aminoacylation, Arginyl-Trna Synthetase, Ligase, Ligase-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Delagoutte, D. Moras, J. Cavarelli
Trna Aminoacylation By Arginyl-Trna Synthetase: Induced Conformations During Substrates Binding
Embo J. V. 19 5599 2000
(for further references see the
PDB file header
)
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Hetero Components
(10, 14)
Info
All Hetero Components
01a: 6-HYDRO-1-METHYLADENOSINE-5'-MONOP... (1MAa)
02a: 1N-METHYLGUANOSINE-5'-MONOPHOSPHAT... (1MGa)
03a: 2N-METHYLGUANOSINE-5'-MONOPHOSPHAT... (2MGa)
04a: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCa)
05a: 5-METHYLURIDINE 5'-MONOPHOSPHATE (5MUa)
06a: ARGININE (ARGa)
07a: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ua)
07b: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ub)
07c: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uc)
08a: N2-DIMETHYLGUANOSINE-5'-MONOPHOSPH... (M2Ga)
09a: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUa)
09b: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUb)
09c: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUc)
10a: SULFATE ION (SO4a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
1MA
1
Mod. Nucleotide
6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2
1MG
1
Mod. Nucleotide
1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
3
2MG
1
Mod. Nucleotide
2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
4
5MC
1
Mod. Nucleotide
5-METHYLCYTIDINE-5'-MONOPHOSPHATE
5
5MU
1
Mod. Nucleotide
5-METHYLURIDINE 5'-MONOPHOSPHATE
6
ARG
1
Mod. Amino Acid
ARGININE
7
H2U
3
Mod. Nucleotide
5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
8
M2G
1
Mod. Nucleotide
N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
9
PSU
3
Mod. Nucleotide
PSEUDOURIDINE-5'-MONOPHOSPHATE
10
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
G B:907 , 5MC B:949 , HOH B:1314 , HOH B:1364
BINDING SITE FOR RESIDUE SO4 B 900
2
AC2
SOFTWARE
GLU A:148 , SER A:151 , ASN A:153 , TYR A:188 , TYR A:347 , ASP A:351 , TYR A:369 , ILE A:371 , GLN A:375 , HOH A:1321 , HOH A:1578 , A B:976
BINDING SITE FOR RESIDUE ARG A 800
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: AA_TRNA_LIGASE_I (A:152-163)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRNA_LIGASE_I
PS00178
Aminoacyl-transfer RNA synthetases class-I signature.
SYRC_YEAST
152-163
1
A:152-163
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Exons
(1, 1)
Info
All Exons
Exon 1.1 (A:2-607)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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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
1.1
YDR341C
1
YDR341C.1
IV:1153621-1151798
1824
SYRC_YEAST
1-607
607
1
A:2-607
606
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SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1f7ua1 (A:484-607)
2a: SCOP_d1f7ua3 (A:2-135)
3a: SCOP_d1f7ua2 (A:136-483)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
(48)
Superfamily
:
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
(48)
Family
:
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
(30)
Protein domain
:
Arginyl-tRNA synthetase (ArgRS)
(4)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
1a
d1f7ua1
A:484-607
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
RRF/tRNA synthetase additional domain-like
(47)
Superfamily
:
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain
(4)
Family
:
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain
(4)
Protein domain
:
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain
(4)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
2a
d1f7ua3
A:2-135
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Nucleotidylyl transferase
(325)
Family
:
Class I aminoacyl-tRNA synthetases (RS), catalytic domain
(137)
Protein domain
:
Arginyl-tRNA synthetase (ArgRS)
(4)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
3a
d1f7ua2
A:136-483
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1f7uA03 (A:2-135)
2a: CATH_1f7uA01 (A:136-482)
3a: CATH_1f7uA02 (A:483-607)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.70, no name defined]
(5)
[unclassified]
(2)
1a
1f7uA03
A:2-135
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
[unclassified]
(27)
2a
1f7uA01
A:136-482
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
Homologous Superfamily
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
[unclassified]
(5)
3a
1f7uA02
A:483-607
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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