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1R6T
Asym. Unit
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:
Select:
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 not available)
All SNPs/Variants
1: VAR_052406 (A54S, chain A, )
2: VAR_036466 (E455D, chain A/B, )
View:
Select:
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:
Select:
Label:
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
(10, 19)
Info
All Exons
Exon 1.3 (A:7-33 | -)
Exon 1.4 (A:34-105 (gaps) | B:97-105)
Exon 1.5 (A:105-141 | B:105-141)
Exon 1.6 (A:141-181 | B:141-181)
Exon 1.7 (A:181-242 | B:181-242)
Exon 1.8 (A:242-276 | B:242-276)
Exon 1.9 (A:276-313 | B:276-313)
Exon 1.10 (A:314-371 | B:314-371 (gaps))
Exon 1.11 (A:372-418 | B:372-418)
Exon 1.12b (A:419-467 | B:419-467)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2a/1.3
02: Boundary 1.3/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12b
11: Boundary 1.12b/-
View:
Label:
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
1.2a
ENST00000392882
2a
ENSE00001513471
chr14:
100841927-100841620
308
SYWC_HUMAN
-
0
0
-
-
1.3
ENST00000392882
3
ENSE00002192528
chr14:
100835595-100835424
172
SYWC_HUMAN
1-33
33
1
A:7-33
-
27
-
1.4
ENST00000392882
4
ENSE00001607458
chr14:
100828258-100828045
214
SYWC_HUMAN
34-105
72
2
A:34-105 (gaps)
B:97-105
72
9
1.5
ENST00000392882
5
ENSE00000941372
chr14:
100826999-100826891
109
SYWC_HUMAN
105-141
37
2
A:105-141
B:105-141
37
37
1.6
ENST00000392882
6
ENSE00000941373
chr14:
100820903-100820784
120
SYWC_HUMAN
141-181
41
2
A:141-181
B:141-181
41
41
1.7
ENST00000392882
7
ENSE00000941374
chr14:
100820206-100820024
183
SYWC_HUMAN
181-242
62
2
A:181-242
B:181-242
62
62
1.8
ENST00000392882
8
ENSE00000941375
chr14:
100813183-100813083
101
SYWC_HUMAN
242-276
35
2
A:242-276
B:242-276
35
35
1.9
ENST00000392882
9
ENSE00000941376
chr14:
100809724-100809612
113
SYWC_HUMAN
276-313
38
2
A:276-313
B:276-313
38
38
1.10
ENST00000392882
10
ENSE00000941377
chr14:
100808908-100808735
174
SYWC_HUMAN
314-371
58
2
A:314-371
B:314-371 (gaps)
58
58
1.11
ENST00000392882
11
ENSE00000941378
chr14:
100803539-100803399
141
SYWC_HUMAN
372-418
47
2
A:372-418
B:372-418
47
47
1.12b
ENST00000392882
12b
ENSE00001314927
chr14:
100801373-100800125
1249
SYWC_HUMAN
419-471
53
2
A:419-467
B:419-467
49
49
[
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]
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1r6ta1 (A:7-60)
2a: SCOP_d1r6ta2 (A:82-467)
2b: SCOP_d1r6tb_ (B:)
View:
Select:
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Classes
(
)
(
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Folds
(
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(
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Superfamilies
(
)
(
)
Families
(
)
(
)
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:
[
close SCOP info
]
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)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
(
)
(
)
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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