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3E9H
Biol. Unit 1
Info
Asym.Unit (337 KB)
Biol.Unit 1 (168 KB)
Biol.Unit 2 (169 KB)
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(1)
Title
:
LYSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH L-LYSYLSULFAMOYL ADENOSINE
Authors
:
H. Sakurama, T. Takita, B. Mikami, T. Itoh, K. Yasukawa, K. Inouye
Date
:
22 Aug 08 (Deposition) - 14 Jul 09 (Release) - 14 Jul 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Aminoacyl Trna Synthetase, Ligase, Protein Biosynthesis, Aminoacyl-Trna Synthetase, Atp-Binding, Cytoplasm, Magnesium, Metal-Binding, Nucleotide-Binding
(Keyword Search:
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Reference
:
H. Sakurama, T. Takita, B. Mikami, T. Itoh, K. Yasukawa, K. Inouye
Two Crystal Structures Of Lysyl-Trna Synthetase From Bacillus Stearothermophilus In Complex With Lysyladenylate-Like Compounds: Insights Into The Irreversible Formation Of The Enzyme-Bound Adenylate Of L-Lysine Hydroxamate
J. Biochem. V. 145 555 2009
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENO... (KAAa)
1b: 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENO... (KAAb)
1c: 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENO... (KAAc)
1d: 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENO... (KAAd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
KAA
2
Ligand/Ion
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:402 , GLU A:404 , GLU A:411 , ASN A:414 , KAA A:2002
BINDING SITE FOR RESIDUE MG A 2001
2
AC2
SOFTWARE
GLY A:207 , GLU A:231 , ARG A:253 , GLU A:255 , ARG A:260 , HIS A:261 , ASN A:262 , PHE A:265 , MET A:267 , GLU A:269 , TYR A:271 , GLU A:411 , HIS A:412 , ALA A:413 , ASN A:414 , PHE A:416 , GLU A:418 , GLY A:463 , GLY A:467 , ARG A:470 , ILE A:481 , HOH A:509 , HOH A:730 , HOH A:846 , MG A:2001
BINDING SITE FOR RESIDUE KAA A 2002
3
AC3
SOFTWARE
ARG B:402 , GLU B:404 , GLU B:411 , ASN B:414 , KAA B:2003
BINDING SITE FOR RESIDUE MG B 2002
4
AC4
SOFTWARE
GLY B:207 , GLU B:231 , ARG B:253 , GLU B:255 , ARG B:260 , HIS B:261 , ASN B:262 , PHE B:265 , MET B:267 , GLU B:269 , TYR B:271 , GLU B:411 , HIS B:412 , ALA B:413 , ASN B:414 , PHE B:416 , GLU B:418 , GLY B:467 , ARG B:470 , ILE B:481 , HOH B:503 , HOH B:963 , MG B:2002
BINDING SITE FOR RESIDUE KAA B 2003
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3e9ha1 (A:4-145)
1b: SCOP_d3e9hb1 (B:4-145)
1c: SCOP_d3e9hc1 (C:4-145)
1d: SCOP_d3e9hd1 (D:4-145)
2a: SCOP_d3e9ha2 (A:146-492)
2b: SCOP_d3e9hb2 (B:146-492)
2c: SCOP_d3e9hc2 (C:146-492)
2d: SCOP_d3e9hd2 (D:146-492)
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Protein Domains
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Organisms
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(
)
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
automated matches
(46)
Protein domain
:
automated matches
(46)
Bacillus stearothermophilus [TaxId: 1422]
(2)
1a
d3e9ha1
A:4-145
1b
d3e9hb1
B:4-145
1c
d3e9hc1
C:4-145
1d
d3e9hd1
D:4-145
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Class II aaRS and biotin synthetases
(165)
Superfamily
:
Class II aaRS and biotin synthetases
(165)
Family
:
automated matches
(17)
Protein domain
:
automated matches
(17)
Bacillus stearothermophilus [TaxId: 1422]
(2)
2a
d3e9ha2
A:146-492
2b
d3e9hb2
B:146-492
2c
d3e9hc2
C:146-492
2d
d3e9hd2
D:146-492
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3e9hA02 (A:146-490)
1b: CATH_3e9hB02 (B:146-490)
1c: CATH_3e9hC02 (C:146-490)
1d: CATH_3e9hD02 (D:146-490)
2a: CATH_3e9hA01 (A:5-145)
2b: CATH_3e9hB01 (B:5-145)
2c: CATH_3e9hC01 (C:5-145)
2d: CATH_3e9hD01 (D:5-145)
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Bacillus stearothermophilus. Organism_taxid: 1422.
(2)
1a
3e9hA02
A:146-490
1b
3e9hB02
B:146-490
1c
3e9hC02
C:146-490
1d
3e9hD02
D:146-490
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Bacillus stearothermophilus. Organism_taxid: 1422.
(2)
2a
3e9hA01
A:5-145
2b
3e9hB01
B:5-145
2c
3e9hC01
C:5-145
2d
3e9hD01
D:5-145
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Pfam Domains
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (337 KB)
Header - Asym.Unit
Biol.Unit 1 (168 KB)
Header - Biol.Unit 1
Biol.Unit 2 (169 KB)
Header - Biol.Unit 2
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