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2QUJ
Asym. Unit
Info
Asym.Unit (137 KB)
Biol.Unit 1 (131 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF HUMAN TRYPTOPHANYL-TRNA SYNTHETASE IN COMPLEX WITH TRPAMP
Authors
:
N. Shen, J. P. Ding
Date
:
05 Aug 07 (Deposition) - 29 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.42
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Aminoacyl-Trna Synthetase, Rossmann Fold, Induced-Fit Mechnism, Atp- Binding, Ligase, Nucleotide-Binding, Protein Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Shen, M. Zhou, B. Yang, Y. Yu, X. Dong, J. Ding
Catalytic Mechanism Of The Tryptophan Activation Reaction Revealed By Crystal Structures Of Human Tryptophanyl-Trna Synthetase In Different Enzymatic States
Nucleic Acids Res. V. 36 1288 2008
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Hetero Components
(4, 15)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
3a: TRYPTOPHAN (TRPa)
4a: TRYPTOPHANYL-5'AMP (TYMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
9
Ligand/Ion
CHLORIDE ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
TRP
1
Mod. Amino Acid
TRYPTOPHAN
4
TYM
1
Ligand/Ion
TRYPTOPHANYL-5'AMP
[
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]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR B:201
BINDING SITE FOR RESIDUE CL B 801
02
AC2
SOFTWARE
HIS A:474
BINDING SITE FOR RESIDUE CL A 802
03
AC3
SOFTWARE
ASN B:118 , ARG B:122
BINDING SITE FOR RESIDUE CL B 803
04
AC4
SOFTWARE
LYS A:204 , ASP A:205
BINDING SITE FOR RESIDUE CL A 805
05
AC5
SOFTWARE
ASP B:113 , LYS B:114
BINDING SITE FOR RESIDUE CL B 808
06
AC6
SOFTWARE
TYR B:159 , THR B:160 , GLY B:161 , ARG B:162 , GLY B:163 , GLN B:194 , GLU B:199 , GLN B:284 , CYS B:309 , GLN B:313 , PHE B:317
BINDING SITE FOR RESIDUE TRP B 817
07
AC7
SOFTWARE
TYR A:159 , THR A:160 , GLY A:161 , ARG A:162 , GLY A:163 , GLY A:172 , PRO A:176 , GLN A:194 , THR A:196 , GLU A:199 , GLN A:284 , CYS A:309 , ALA A:310 , GLN A:313 , PHE A:317 , PHE A:340 , LYS A:349
BINDING SITE FOR RESIDUE TYM A 810
08
AC8
SOFTWARE
LYS A:253 , THR B:207 , LEU B:208 , ASP B:209
BINDING SITE FOR RESIDUE GOL B 812
09
AC9
SOFTWARE
THR A:207 , LEU A:208 , ASP A:209 , LYS B:253
BINDING SITE FOR RESIDUE GOL A 813
10
BC1
SOFTWARE
GLY A:380 , ARG A:381 , ASP A:382 , LEU A:426 , THR A:427
BINDING SITE FOR RESIDUE GOL A 814
11
BC2
SOFTWARE
GLN B:126 , ARG B:381 , ASP B:382 , THR B:383 , LEU B:426 , THR B:427 , GLY B:428
BINDING SITE FOR RESIDUE GOL B 815
[
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]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: 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_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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 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
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
(9, 18)
Info
All Exons
Exon 1.4 (A:88-105 | B:94-105)
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)
Exon 1.11 (A:372-418 | B:372-418)
Exon 1.12b (A:419-471 | B:419-471)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.4
02: Boundary 1.4/1.5
03: Boundary 1.5/1.6
04: Boundary 1.6/1.7
05: Boundary 1.7/1.8
06: Boundary 1.8/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12b
10: 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
0
-
-
1.4
ENST00000392882
4
ENSE00001607458
chr14:
100828258-100828045
214
SYWC_HUMAN
34-105
72
2
A:88-105
B:94-105
18
12
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
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:419-471
B:419-471
53
53
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2quja_ (A:)
1b: SCOP_d2qujb_ (B:)
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)
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(
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Superfamilies
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
1a
d2quja_
A:
1b
d2qujb_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2qujB01 (B:94-350)
1b: CATH_2qujA01 (A:88-350)
2a: CATH_2qujB02 (B:351-471)
2b: CATH_2qujA02 (A:351-475)
View:
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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
2qujB01
B:94-350
1b
2qujA01
A:88-350
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Tyrosyl-Transfer RNA Synthetase
(70)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase
(70)
Human (Homo sapiens)
(11)
2a
2qujB02
B:351-471
2b
2qujA02
A:351-475
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_tRNA_synt_1b_2qujB01 (B:151-443)
1b: PFAM_tRNA_synt_1b_2qujB02 (B:151-443)
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Organisms
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)
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)
Clan
:
HUP
(230)
Family
:
tRNA-synt_1b
(51)
Homo sapiens (Human)
(10)
1a
tRNA-synt_1b-2qujB01
B:151-443
1b
tRNA-synt_1b-2qujB02
B:151-443
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Asymmetric Unit 1
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