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2AZX
Asym. Unit
Info
Asym.Unit (199 KB)
Biol.Unit 1 (190 KB)
Biol.Unit 2 (192 KB)
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(1)
Title
:
CHARGED AND UNCHARGED TRNAS ADOPT DISTINCT CONFORMATIONS WHEN COMPLEXED WITH HUMAN TRYPTOPHANYL-TRNA SYNTHETASE
Authors
:
X. L. Yang, F. J. Otero, K. L. Ewalt, J. Liu, M. A. Swairjo, C. Kohrer, U. L. Rajbhandary, R. J. Skene, D. E. Mcree, P. Schimmel
Date
:
12 Sep 05 (Deposition) - 01 Aug 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (2x)
Biol. Unit 2: B,D (2x)
Keywords
:
Two Synthetase-Trna Complex With Distinct Conformations, Association Complex And Dissociation Complex, Ligase-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. L. Yang, F. J. Otero, K. L. Ewalt, J. Liu, M. A. Swairjo, C. Kohrer, U. L. Rajbhandary, R. J. Skene, D. E. Mcree, P. Schimmel
Two Conformations Of A Crystalline Human Trna Synthetase-Trna Complex: Implications For Protein Synthesis
Embo J. V. 25 2919 2006
[
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Hetero Components
(5, 36)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: MAGNESIUM ION (MGa)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
5a: TRYPTOPHAN (TRPa)
5b: TRYPTOPHAN (TRPb)
5c: TRYPTOPHAN (TRPc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
10
Ligand/Ion
SULFATE ION
5
TRP
3
Mod. Amino Acid
TRYPTOPHAN
[
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS B:170 , HIS B:173 , SER B:351 , ALA B:352
BINDING SITE FOR RESIDUE SO4 B 701
02
AC2
SOFTWARE
HIS A:170 , HIS A:173 , LYS A:349 , MSE A:350 , SER A:351 , ALA A:352 , SER A:353
BINDING SITE FOR RESIDUE SO4 A 702
03
AC3
SOFTWARE
ASP B:142 , MSE B:143 , ASN B:144 , GLN B:145 , HOH B:1009
BINDING SITE FOR RESIDUE SO4 B 703
04
AC4
SOFTWARE
HIS A:140 , ASP A:142 , ASN A:144 , GLN A:145
BINDING SITE FOR RESIDUE SO4 A 704
05
AC5
SOFTWARE
ALA B:352 , PRO B:355 , ASN B:356 , PHE B:360 , MG B:901
BINDING SITE FOR RESIDUE SO4 B 705
06
AC6
SOFTWARE
ARG B:141 , ARG B:321 , LYS B:331
BINDING SITE FOR RESIDUE SO4 B 706
07
AC7
SOFTWARE
ASP A:354 , PRO A:355 , ASN A:356
BINDING SITE FOR RESIDUE SO4 A 707
08
AC8
SOFTWARE
THR A:207 , LEU A:208 , ASP A:209 , LYS A:253
BINDING SITE FOR RESIDUE SO4 A 708
09
AC9
SOFTWARE
THR B:364 , ALA B:365
BINDING SITE FOR RESIDUE SO4 B 709
10
BC1
SOFTWARE
THR B:453 , ASP B:454 , GLU B:455
BINDING SITE FOR RESIDUE SO4 B 710
11
BC2
SOFTWARE
SER B:351 , ASP B:354 , SER B:357 , SER B:358 , SO4 B:705
BINDING SITE FOR RESIDUE MG B 901
12
BC3
SOFTWARE
TYR A:159 , THR A:160 , GLY A:161 , ARG A:162 , GLY A:163 , GLN A:194 , THR A:196 , GLU A:199 , GLN A:284 , CYS A:309 , GLN A:313 , PHE A:317
BINDING SITE FOR RESIDUE TRP A 601
13
BC4
SOFTWARE
LEU A:174 , ILE A:178 , PHE A:406 , GLU A:408 , LEU A:441 , ARG A:448
BINDING SITE FOR RESIDUE TRP A 602
14
BC5
SOFTWARE
TYR B:159 , THR B:160 , GLY B:161 , ARG B:162 , GLY B:163 , GLN B:194 , THR B:196 , GLU B:199 , GLN B:284 , CYS B:309 , GLN B:313 , PHE B:317 , HOH B:1005
BINDING SITE FOR RESIDUE TRP B 603
15
BC6
SOFTWARE
THR B:207 , LEU B:208 , ASP B:209 , LYS B:253 , HOH B:1021
BINDING SITE FOR RESIDUE GOL B 801
[
close Site info
]
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:82-105 | B:82-105)
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:419-468 | B:419-469)
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:82-105
B:82-105
24
24
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:419-468
B:419-469
50
51
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2azxa1 (A:82-468)
1b: SCOP_d2azxb1 (B:82-468)
View:
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Classes
(
)
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Folds
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(
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Superfamilies
(
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(
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Families
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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
d2azxa1
A:82-468
1b
d2azxb1
B:82-468
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2azxA01 (A:82-339)
1b: CATH_2azxB01 (B:82-339)
2a: CATH_2azxA02 (A:340-468)
2b: CATH_2azxB02 (B:340-469)
View:
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Topologies
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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)
[unclassified]
(27)
1a
2azxA01
A:82-339
1b
2azxB01
B:82-339
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Tyrosyl-Transfer RNA Synthetase
(70)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase
(70)
[unclassified]
(2)
2a
2azxA02
A:340-468
2b
2azxB02
B:340-469
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
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Sidechain
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Protein & NOT PROSITE
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Chain C
Chain D
Asymmetric Unit 1
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Asym.Unit (199 KB)
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