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Asym. Unit
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Asym.Unit (158 KB)
Biol.Unit 1 (153 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LEUCYL-TRNA SYNTHETASE FROM THE ARCHAEON PYROCOCCUS HORIKOSHII REVEALS A NOVEL EDITING DOMAIN ORIENTATION
Authors
:
R. Fukunaga, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
30 May 04 (Deposition) - 08 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Leucyl-Trna Synthetase, Leucine, Aminoacyl-Trna, Editing, Amino Acid, Aminoacylation, Pyrococcus Horikoshii, Trnaleu, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase
(Keyword Search:
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Reference
:
R. Fukunaga, S. Yokoyama
Crystal Structure Of Leucyl-Trna Synthetase From The Archaeon Pyrococcus Horikoshii Reveals A Novel Editing Domain Orientation
J. Mol. Biol. V. 346 57 2005
(for further references see the
PDB file header
)
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Hetero Components
(1, 8)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
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No.
Name
Count
Type
Full Name
1
SO4
8
Ligand/Ion
SULFATE ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:84 , SER A:85 , PRO A:86 , HIS A:196 , ARG A:510 , HOH A:943 , HOH A:994 , HOH A:1059 , HOH A:1189
BINDING SITE FOR RESIDUE SO4 A 901
2
AC2
SOFTWARE
SER A:652 , LYS A:653 , SER A:654 , HOH A:1715
BINDING SITE FOR RESIDUE SO4 A 902
3
AC3
SOFTWARE
ARG A:93 , GLU A:200 , GLY A:201 , GLU A:202 , ASP A:203
BINDING SITE FOR RESIDUE SO4 A 903
4
AC4
SOFTWARE
ARG A:492 , LYS A:611 , HOH A:1101 , HOH A:1235
BINDING SITE FOR RESIDUE SO4 A 904
5
AC5
SOFTWARE
LYS A:506 , ARG A:510 , HOH A:1079 , HOH A:1260 , HOH A:1475
BINDING SITE FOR RESIDUE SO4 A 905
6
AC6
SOFTWARE
ARG A:182 , ARG A:184 , ILE A:206 , HOH A:1046 , HOH A:1515
BINDING SITE FOR RESIDUE SO4 A 906
7
AC7
SOFTWARE
THR A:229 , LEU A:230 , ARG A:231 , TYR A:401 , HOH A:1488
BINDING SITE FOR RESIDUE SO4 A 907
8
AC8
SOFTWARE
TRP A:185 , GLY A:190 , PHE A:275 , LYS A:459 , HOH A:971 , HOH A:1104 , HOH A:1484
BINDING SITE FOR RESIDUE SO4 A 908
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: AA_TRNA_LIGASE_I (A:43-54)
;
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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.
SYL_PYRHO
43-54
1
A:43-54
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1wkbA01 (A:4-204,A:448-689)
2a: CATH_1wkbA02 (A:205-447)
3a: CATH_1wkbA03 (A:690-810)
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Homologous Superfamilies
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)
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)
Pyrococcus horikoshii. Organism_taxid: 53953.
(3)
1a
1wkbA01
A:4-204,A:448-689
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Isoleucyl-tRNA Synthetase; domain 2
(21)
Homologous Superfamily
:
Isoleucyl-tRNA Synthetase; Domain 2
(21)
Pyrococcus horikoshii. Organism_taxid: 53953.
(1)
2a
1wkbA02
A:205-447
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
Homologous Superfamily
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
Pyrococcus horikoshii. Organism_taxid: 53953.
(1)
3a
1wkbA03
A:690-810
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_tRNA_synt_1_1wkbA01 (A:12-690)
2a: PFAM_Anticodon_1_1wkbA02 (A:726-810)
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(
)
Clan
:
HUP
(230)
Family
:
tRNA-synt_1
(17)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
(1)
1a
tRNA-synt_1-1wkbA01
A:12-690
Clan
:
no clan defined [family: Anticodon_1]
(10)
Family
:
Anticodon_1
(10)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
(1)
2a
Anticodon_1-1wkbA02
A:726-810
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Asymmetric Unit 1
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