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1R6T
Biol. Unit 1
Info
Asym.Unit (144 KB)
Biol.Unit 1 (137 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN TRYPTOPHANYL-TRNA SYNTHETASE
Authors
:
X. -L. Yang, F. J. Otero, R. J. Skene, D. E. Mcree, L. Ribas De Pouplana, P. Schimmel
Date
:
16 Oct 03 (Deposition) - 06 Jan 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Class Ic Trna Synthetase, Rossmann Fold Catalytical Domain, Anticodon Recognition Domain, Bound Trp-Amp, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. -L. Yang, F. J. Otero, R. J. Skene, D. E. Mcree, P. Schimmel, L. Ribas De Pouplana
Crystal Structures That Suggest Late Development Of Genetic Code Components For Differentiating Aromatic Side Chains
Proc. Natl. Acad. Sci. Usa V. 100 15376 2003
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
3a: TRYPTOPHANYL-5'AMP (TYMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
MSE
21
Mod. Amino Acid
SELENOMETHIONINE
3
TYM
1
Ligand/Ion
TRYPTOPHANYL-5'AMP
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:159 , THR A:160 , GLY A:161 , ARG A:162 , GLY A:163 , GLY A:172 , HIS A:173 , PRO A:176 , GLN A:194 , GLU A:199 , GLN A:284 , ALA A:310 , ASP A:312 , GLN A:313 , PHE A:317 , PHE A:339 , PHE A:340 , LYS A:349 , MSE A:350 , HOH A:1002 , HOH A:1007 , HOH A:1018 , HOH A:1028 , HOH A:1044 , HOH A:1113
BINDING SITE FOR RESIDUE TYM A 501
2
AC2
SOFTWARE
LYS A:253 , ARG A:326 , ILE A:327 , TYR B:201 , THR B:207 , LEU B:208 , HOH B:1138 , HOH B:1213 , HOH B:1285
BINDING SITE FOR RESIDUE GOL B 601
3
AC3
SOFTWARE
ASP A:101 , LYS A:111 , GLY A:135 , PHE A:138
BINDING SITE FOR RESIDUE GOL A 602
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SAPs(SNPs)/Variants
(2, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_052406 (A54S, chain A, )
2: VAR_036466 (E455D, chain A/B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_052406
A
54
S
SYWC_HUMAN
Polymorphism
2234521
A
A
54
S
2
UniProt
VAR_036466
E
455
D
SYWC_HUMAN
Unclassified
---
A/B
E
455
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 4)
Info
All PROSITE Patterns/Profiles
1: WHEP_TRS_2 (A:8-60)
2: WHEP_TRS_1 (A:19-47)
3: AA_TRNA_LIGASE_I (A:164-174,B:164-174)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
WHEP_TRS_2
PS51185
WHEP-TRS domain profile.
SYWC_HUMAN
8-64
1
A:8-60
2
WHEP_TRS_1
PS00762
WHEP-TRS domain signature.
SYWC_HUMAN
19-47
1
A:19-47
3
AA_TRNA_LIGASE_I
PS00178
Aminoacyl-transfer RNA synthetases class-I signature.
SYWC_HUMAN
164-174
2
A:164-174
B:164-174
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1r6ta1 (A:7-60)
2a: SCOP_d1r6ta2 (A:82-467)
2b: SCOP_d1r6tb_ (B:)
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(
)
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(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
S15/NS1 RNA-binding domain
(66)
Superfamily
:
S15/NS1 RNA-binding domain
(66)
Family
:
a tRNA synthase domain
(4)
Protein domain
:
N-terminal domain of eukaryotic tryptophanyl-tRNA synthetase (TrpRS)
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1r6ta1
A:7-60
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)
Human (Homo sapiens) [TaxId: 9606]
(11)
2a
d1r6ta2
A:82-467
2b
d1r6tb_
B:
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CATH Domains
(3, 5)
Info
all CATH domains
1a: CATH_1r6tB01 (B:97-345)
1b: CATH_1r6tA02 (A:82-353)
2a: CATH_1r6tA01 (A:7-60)
3a: CATH_1r6tB02 (B:355-467)
3b: CATH_1r6tA03 (A:354-467)
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)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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)
Human (Homo sapiens)
(27)
1a
1r6tB01
B:97-345
1b
1r6tA02
A:82-353
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.10, no name defined]
(116)
Human (Homo sapiens)
(2)
2a
1r6tA01
A:7-60
Topology
:
Tyrosyl-Transfer RNA Synthetase
(70)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase
(70)
Human (Homo sapiens)
(11)
3a
1r6tB02
B:355-467
3b
1r6tA03
A:354-467
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_tRNA_synt_1b_1r6tB01 (B:151-443)
1b: PFAM_tRNA_synt_1b_1r6tB02 (B:151-443)
2a: PFAM_WHEP_TRS_1r6tA01 (A:12-60)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
HUP
(230)
Family
:
tRNA-synt_1b
(51)
Homo sapiens (Human)
(10)
1a
tRNA-synt_1b-1r6tB01
B:151-443
1b
tRNA-synt_1b-1r6tB02
B:151-443
Clan
:
no clan defined [family: WHEP-TRS]
(3)
Family
:
WHEP-TRS
(3)
Homo sapiens (Human)
(2)
2a
WHEP-TRS-1r6tA01
A:12-60
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Asymmetric Unit 1
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