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1VBN
Biol. Unit 1
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Asym.Unit (112 KB)
Biol.Unit 1 (107 KB)
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(1)
Title
:
ESCHERICHIA COLI TYROSYL-TRNA SYNTHETASE MUTANT COMPLEXED WITH TYR-AMS
Authors
:
T. Kobayashi, K. Sakamoto, T. Takimura, K. Kamata, R. Sekine, S. Nishim S. Yokoyama, Riken Structural Genomics/Proteomics Initiative
Date
:
27 Feb 04 (Deposition) - 25 Jan 05 (Release) - 28 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Ligase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
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Reference
:
T. Kobayashi, K. Sakamoto, T. Takimura, R. Sekine, K. Vincent, K. Kamata, S. Nishimura, S. Yokoyama
Structural Basis Of Nonnatural Amino Acid Recognition By An Engineered Aminoacyl-Trna Synthetase For Genetic Code Expansion
Proc. Natl. Acad. Sci. Usa V. 102 1366 2005
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENO... (YSAa)
1b: 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENO... (YSAb)
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No.
Name
Count
Type
Full Name
1
YSA
2
Ligand/Ion
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE
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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
GLY A:39 , ASP A:41 , GLY A:50 , HIS A:51 , VAL A:53 , PRO A:54 , THR A:76 , ASP A:81 , TYR A:175 , GLN A:179 , ASP A:182 , GLY A:198 , ASP A:200 , GLN A:201 , PRO A:226 , LEU A:227 , ILE A:228 , HOH A:1010
BINDING SITE FOR RESIDUE YSA A 1001
2
AC2
SOFTWARE
GLY B:39 , ASP B:41 , GLY B:50 , HIS B:51 , VAL B:53 , PRO B:54 , LEU B:71 , ASP B:81 , TYR B:175 , GLN B:179 , ASP B:182 , GLY B:197 , GLY B:198 , ASP B:200 , GLN B:201 , PRO B:226 , LEU B:227 , ILE B:228
BINDING SITE FOR RESIDUE YSA B 1002
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: AA_TRNA_LIGASE_I (A:42-52,B:42-52)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRNA_LIGASE_I
PS00178
Aminoacyl-transfer RNA synthetases class-I signature.
SYY_ECOLI
42-52
2
A:42-52
B:42-52
SYY_ECO57
42-52
2
A:42-52
B:42-52
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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.
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1vbna_ (A:)
1b: SCOP_d1vbnb_ (B:)
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Protein Domains
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(
)
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
:
automated matches
(22)
Escherichia coli [TaxId: 562]
(3)
1a
d1vbna_
A:
1b
d1vbnb_
B:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1vbnA01 (A:5-227)
1b: CATH_1vbnB01 (B:5-227)
2a: CATH_1vbnA02 (A:228-322)
2b: CATH_1vbnB02 (B:228-322)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Escherichia coli. Organism_taxid: 562.
(13)
1a
1vbnA01
A:5-227
1b
1vbnB01
B:5-227
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Tyrosyl-Transfer RNA Synthetase
(70)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase
(70)
Escherichia coli. Organism_taxid: 562.
(3)
2a
1vbnA02
A:228-322
2b
1vbnB02
B:228-322
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_tRNA_synt_1b_1vbnB01 (B:29-322)
1b: PFAM_tRNA_synt_1b_1vbnB02 (B:29-322)
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Clan
:
HUP
(230)
Family
:
tRNA-synt_1b
(51)
Escherichia coli (strain K12)
(6)
1a
tRNA-synt_1b-1vbnB01
B:29-322
1b
tRNA-synt_1b-1vbnB02
B:29-322
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Asymmetric Unit 1
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Asym.Unit (112 KB)
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