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1Q11
Asym. Unit
Info
Asym.Unit (66 KB)
Biol.Unit 1 (121 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AN ACTIVE FRAGMENT OF HUMAN TYROSYL-TRNA SYNTHETASE WITH TYROSINOL
Authors
:
X. -L. Yang, P. Schimmel, L. Ribas De Pouplana
Date
:
18 Jul 03 (Deposition) - 06 Jan 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Rossmann Fold Domain Containing The Active Site, Anticodon Recognition Domain, Substrate Analog Tyrosinol Co-Crystalized, 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
(4, 5)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: POTASSIUM ION (Ka)
3a: PHOSPHATE ION (PO4a)
4a: 4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PH... (TYEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
K
1
Ligand/Ion
POTASSIUM ION
3
PO4
1
Ligand/Ion
PHOSPHATE ION
4
TYE
1
Ligand/Ion
4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL
[
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:305 , PRO A:306 , GLY A:307 , ASP A:308 , HOH A:1044 , HOH A:1186 , HOH A:1263
BINDING SITE FOR RESIDUE PO4 A 501
2
AC2
SOFTWARE
THR A:42 , ALA A:43 , THR A:45 , TYR A:52 , TYR A:97 , HOH A:1011
BINDING SITE FOR RESIDUE K A 701
3
AC3
SOFTWARE
TYR A:39 , GLY A:41 , LEU A:72 , ALA A:74 , HIS A:77 , VAL A:152 , TYR A:166 , GLN A:170 , ASP A:173 , GLN A:182 , GLN A:188 , HOH A:1165
BINDING SITE FOR RESIDUE TYE A 401
4
AC4
SOFTWARE
HIS A:12 , ARG A:16 , HOH A:1155
BINDING SITE FOR RESIDUE GOL A 601
5
AC5
SOFTWARE
LYS A:127 , GLU A:128 , HIS A:143 , LYS A:146
BINDING SITE FOR RESIDUE GOL A 602
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_026681 (G41R, chain A, )
2: VAR_026683 (Q170H, chain A, )
3: VAR_026684 (E196K, chain A, )
4: VAR_073292 (E274K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_026681
G
41
R
SYYC_HUMAN
Disease (CMTDIC)
---
A
G
41
R
2
UniProt
VAR_026683
Q
170
H
SYYC_HUMAN
Polymorphism
2128600
A
Q
170
H
3
UniProt
VAR_026684
E
196
K
SYYC_HUMAN
Disease (CMTDIC)
---
A
E
196
K
4
UniProt
VAR_073292
E
274
K
SYYC_HUMAN
Unclassified
---
A
E
274
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(9, 9)
Info
All Exons
Exon 1.1a (A:4-19)
Exon 1.2b (A:20-68)
Exon 1.3b (A:69-127)
Exon 1.4a (A:127-170)
Exon 1.5b (A:171-197)
Exon 1.7a (A:198-220)
Exon 1.8 (A:231-274)
Exon 1.9c (A:274-302)
Exon 1.10b (A:303-342)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2b
03: Boundary 1.2b/1.3b
04: Boundary 1.3b/1.4a
05: Boundary 1.4a/1.5b
06: Boundary 1.5b/1.7a
07: Boundary 1.7a/1.8
08: Boundary 1.8/1.9c
09: Boundary 1.9c/1.10b
10: Boundary 1.10b/1.11b
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
1.1a
ENST00000373477
1a
ENSE00001460665
chr1:
33283754-33282789
966
SYYC_HUMAN
1-19
19
1
A:4-19
16
1.2b
ENST00000373477
2b
ENSE00001208748
chr1:
33276658-33276512
147
SYYC_HUMAN
20-68
49
1
A:20-68
49
1.3b
ENST00000373477
3b
ENSE00001208739
chr1:
33276367-33276192
176
SYYC_HUMAN
69-127
59
1
A:69-127
59
1.4a
ENST00000373477
4a
ENSE00001208728
chr1:
33272212-33272083
130
SYYC_HUMAN
127-170
44
1
A:127-170
44
1.5b
ENST00000373477
5b
ENSE00001208722
chr1:
33263444-33263364
81
SYYC_HUMAN
171-197
27
1
A:171-197
27
1.7a
ENST00000373477
7a
ENSE00001208715
chr1:
33256855-33256763
93
SYYC_HUMAN
198-228
31
1
A:198-220
23
1.8
ENST00000373477
8
ENSE00000916656
chr1:
33252676-33252541
136
SYYC_HUMAN
229-274
46
1
A:231-274
44
1.9c
ENST00000373477
9c
ENSE00000916655
chr1:
33252048-33251963
86
SYYC_HUMAN
274-302
29
1
A:274-302
29
1.10b
ENST00000373477
10b
ENSE00001065998
chr1:
33248140-33248005
136
SYYC_HUMAN
303-348
46
1
A:303-342
40
1.11b
ENST00000373477
11b
ENSE00001065997
chr1:
33246746-33246649
98
SYYC_HUMAN
348-380
33
0
-
-
1.12b
ENST00000373477
12b
ENSE00001168511
chr1:
33245879-33245686
194
SYYC_HUMAN
381-445
65
0
-
-
1.12c
ENST00000373477
12c
ENSE00001065999
chr1:
33245124-33244983
142
SYYC_HUMAN
445-492
48
0
-
-
1.13d
ENST00000373477
13d
ENSE00001460663
chr1:
33241692-33240840
853
SYYC_HUMAN
493-528
36
0
-
-
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1q11a_ (A:)
View:
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(
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Folds
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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
:
Tyrosyl-tRNA synthetase (TyrRS)
(25)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1q11a_
A:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1q11A01 (A:5-213)
2a: CATH_1q11A02 (A:217-342)
View:
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Classes
(
)
(
)
Architectures
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(
)
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
1q11A01
A:5-213
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
1q11A02
A:217-342
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_tRNA_synt_1b_1q11A01 (A:31-322)
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Clans
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Families
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(
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Organisms
(
)
(
)
Clan
:
HUP
(230)
Family
:
tRNA-synt_1b
(51)
Homo sapiens (Human)
(10)
1a
tRNA-synt_1b-1q11A01
A:31-322
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Asymmetric Unit 1
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