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3KT3
Asym. Unit
Info
Asym.Unit (534 KB)
Biol.Unit 1 (267 KB)
Biol.Unit 2 (266 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF S. CEREVISIAE TRYPTOPHANYL-TRNA SYNTHETASE IN COMPLEX WITH TRPAMP
Authors
:
M. Zhou, X. Dong, C. Zhong, N. Shen, J. Ding
Date
:
24 Nov 09 (Deposition) - 16 Feb 10 (Release) - 16 Jun 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Tryptophanyl-Trna Synthetase, S. Cerevisiae, Sulfate Ion, Amino Acid Activation, Catalytic Mechanism, Aminoacyl-Trna Synthetase, Atp- Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
M. Zhou, X. Dong, N. Shen, C. Zhong, J. Ding
Crystal Structures Of Saccharomyces Cerevisiae Tryptophanyl-Trna Synthetase: New Insights Into The Mechanism Of Tryptophan Activation And Implications For Anti-Fungal Drug Design
Nucleic Acids Res. V. 38 3399 2010
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Hetero Components
(2, 17)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
1l: SULFATE ION (SO4l)
1m: SULFATE ION (SO4m)
2a: TRYPTOPHANYL-5'AMP (TYMa)
2b: TRYPTOPHANYL-5'AMP (TYMb)
2c: TRYPTOPHANYL-5'AMP (TYMc)
2d: TRYPTOPHANYL-5'AMP (TYMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
13
Ligand/Ion
SULFATE ION
2
TYM
4
Ligand/Ion
TRYPTOPHANYL-5'AMP
[
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Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:106 , GLY A:108 , ARG A:109 , GLY A:110 , GLY A:119 , HIS A:120 , PRO A:123 , GLU A:141 , THR A:143 , GLU A:146 , LYS A:147 , GLN A:230 , CYS A:255 , ALA A:256 , ASP A:258 , GLN A:259 , PHE A:263 , ARG A:284 , PHE A:285 , PHE A:286 , LYS A:295 , MET A:296 , SO4 A:439 , HOH A:464 , HOH A:490
BINDING SITE FOR RESIDUE TYM A 500
02
AC2
SOFTWARE
ARG A:109 , HIS A:117 , HIS A:120 , SER A:297 , ALA A:298 , TYM A:500
BINDING SITE FOR RESIDUE SO4 A 439
03
AC3
SOFTWARE
ALA A:42 , GLN A:43 , ASN A:44
BINDING SITE FOR RESIDUE SO4 A 440
04
AC4
SOFTWARE
ARG A:73 , GLU A:74 , HOH A:504
BINDING SITE FOR RESIDUE SO4 A 441
05
AC5
SOFTWARE
PHE A:148 , THR A:155 , ILE A:156 , HOH A:448 , ARG B:199 , ARG B:202
BINDING SITE FOR RESIDUE SO4 A 442
06
AC6
SOFTWARE
TYR B:106 , THR B:107 , GLY B:108 , ARG B:109 , GLY B:110 , GLY B:119 , HIS B:120 , PRO B:123 , GLU B:141 , THR B:143 , GLU B:146 , LYS B:147 , GLN B:230 , CYS B:255 , ALA B:256 , ASP B:258 , GLN B:259 , PHE B:263 , PHE B:286 , LYS B:295 , MET B:296 , SO4 B:439 , HOH B:461 , HOH B:466
BINDING SITE FOR RESIDUE TYM B 700
07
AC7
SOFTWARE
ARG B:109 , HIS B:117 , HIS B:120 , LYS B:295 , MET B:296 , SER B:297 , ALA B:298 , TYM B:700
BINDING SITE FOR RESIDUE SO4 B 439
08
AC8
SOFTWARE
ARG A:199 , PHE B:148 , THR B:155 , ILE B:156
BINDING SITE FOR RESIDUE SO4 B 440
09
AC9
SOFTWARE
ARG B:73 , GLU B:74
BINDING SITE FOR RESIDUE SO4 B 441
10
BC1
SOFTWARE
TYR C:106 , THR C:107 , GLY C:108 , ARG C:109 , GLY C:110 , GLY C:119 , HIS C:120 , PRO C:123 , GLU C:141 , THR C:143 , GLU C:146 , LYS C:147 , GLN C:230 , CYS C:255 , ALA C:256 , ASP C:258 , GLN C:259 , PHE C:263 , PHE C:285 , PHE C:286 , LYS C:295 , MET C:296 , SO4 C:441 , HOH C:446 , HOH C:463
BINDING SITE FOR RESIDUE TYM C 600
11
BC2
SOFTWARE
ARG C:73 , GLU C:74
BINDING SITE FOR RESIDUE SO4 C 439
12
BC3
SOFTWARE
THR C:155 , ILE C:156 , ARG D:199
BINDING SITE FOR RESIDUE SO4 C 440
13
BC4
SOFTWARE
ARG C:109 , HIS C:117 , HIS C:120 , LYS C:295 , MET C:296 , SER C:297 , ALA C:298 , TYM C:600
BINDING SITE FOR RESIDUE SO4 C 441
14
BC5
SOFTWARE
TYR D:106 , THR D:107 , GLY D:108 , ARG D:109 , GLY D:110 , GLY D:119 , HIS D:120 , PRO D:123 , GLU D:141 , THR D:143 , GLU D:146 , LYS D:147 , GLN D:230 , CYS D:255 , ALA D:256 , ASP D:258 , GLN D:259 , PHE D:263 , ARG D:284 , PHE D:285 , PHE D:286 , LYS D:295 , MET D:296 , SO4 D:439
BINDING SITE FOR RESIDUE TYM D 800
15
BC6
SOFTWARE
ARG D:109 , HIS D:117 , HIS D:120 , SER D:297 , ALA D:298 , TYM D:800
BINDING SITE FOR RESIDUE SO4 D 439
16
BC7
SOFTWARE
ARG D:73 , GLU D:74
BINDING SITE FOR RESIDUE SO4 D 440
17
BC8
SOFTWARE
ARG C:199 , PHE D:148 , THR D:155 , ILE D:156 , HOH D:454
BINDING SITE FOR RESIDUE SO4 D 441
[
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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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: AA_TRNA_LIGASE_I (A:111-121,B:111-121,C:111-121,D:11...)
;
View:
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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.
SYWC_YEAST
111-121
4
A:111-121
B:111-121
C:111-121
D:111-121
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Exons
(1, 4)
Info
All Exons
Exon 1.1 (A:17-425 | B:21-425 | C:23-425 | D...)
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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
YOL097C
1
YOL097C.1
XV:137825-136527
1299
SYWC_YEAST
1-432
432
4
A:17-425
B:21-425
C:23-425
D:17-425
409
405
403
409
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3kt3a_ (A:)
1b: SCOP_d3kt3b_ (B:)
1c: SCOP_d3kt3c_ (C:)
1d: SCOP_d3kt3d_ (D:)
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Protein Domains
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Organisms
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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
:
Tryptophanyl-tRNA synthetase (TrpRS)
(28)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(4)
1a
d3kt3a_
A:
1b
d3kt3b_
B:
1c
d3kt3c_
C:
1d
d3kt3d_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_tRNA_synt_1b_3kt3D01 (D:246-389)
1b: PFAM_tRNA_synt_1b_3kt3D02 (D:246-389)
1c: PFAM_tRNA_synt_1b_3kt3D03 (D:246-389)
1d: PFAM_tRNA_synt_1b_3kt3D04 (D:246-389)
1e: PFAM_tRNA_synt_1b_3kt3D05 (D:246-389)
1f: PFAM_tRNA_synt_1b_3kt3D06 (D:246-389)
1g: PFAM_tRNA_synt_1b_3kt3D07 (D:246-389)
1h: PFAM_tRNA_synt_1b_3kt3D08 (D:246-389)
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Clan
:
HUP
(230)
Family
:
tRNA-synt_1b
(51)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
1a
tRNA-synt_1b-3kt3D01
D:246-389
1b
tRNA-synt_1b-3kt3D02
D:246-389
1c
tRNA-synt_1b-3kt3D03
D:246-389
1d
tRNA-synt_1b-3kt3D04
D:246-389
1e
tRNA-synt_1b-3kt3D05
D:246-389
1f
tRNA-synt_1b-3kt3D06
D:246-389
1g
tRNA-synt_1b-3kt3D07
D:246-389
1h
tRNA-synt_1b-3kt3D08
D:246-389
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