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3E9I
Biol. Unit 1
Info
Asym.Unit (339 KB)
Biol.Unit 1 (170 KB)
Biol.Unit 2 (170 KB)
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(1)
Title
:
LYSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH L-LYSINE HYDROXAMATE-AMP
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
:
2.20
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, Atp-Binding, Cytoplasm, Magnesium, Metal-Binding, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
(2, 4)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: 5'-O-{(R)-HYDROXY[(L-LYSYLAMINO)OX... (XAHa)
3b: 5'-O-{(R)-HYDROXY[(L-LYSYLAMINO)OX... (XAHb)
3c: 5'-O-{(R)-HYDROXY[(L-LYSYLAMINO)OX... (XAHc)
3d: 5'-O-{(R)-HYDROXY[(L-LYSYLAMINO)OX... (XAHd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
XAH
2
Ligand/Ion
5'-O-{(R)-HYDROXY[(L-LYSYLAMINO)OXY]PHOSPHORYL}ADENOSINE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:404 , GLU A:411 , ASN A:414 , XAH A:1001
BINDING SITE FOR RESIDUE MG A 1000
2
AC2
SOFTWARE
GLY A:207 , ALA A:208 , ALA A:229 , 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:467 , ARG A:470 , ILE A:481 , HOH A:581 , MG A:1000
BINDING SITE FOR RESIDUE XAH A 1001
3
AC3
SOFTWARE
ARG A:186 , ASP A:189 , SER A:190 , TYR A:193 , LEU A:194 , GLU A:195 , HOH A:545 , GLN B:182 , HOH B:977
BINDING SITE FOR RESIDUE 1PE A 494
4
AC4
SOFTWARE
GLU B:404 , GLU B:411 , ASN B:414 , XAH B:1101
BINDING SITE FOR RESIDUE MG B 1100
5
AC5
SOFTWARE
GLY B:207 , ALA B:208 , ALA B:229 , GLU B:231 , ARG B:253 , GLU B:255 , ARG B:260 , HIS B:261 , ASN B:262 , PHE B:265 , 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 , HOH B:706 , MG B:1100
BINDING SITE FOR RESIDUE XAH B 1101
6
AC6
SOFTWARE
LEU A:179 , GLN A:182 , ARG A:186 , GLU A:294 , ASP B:189 , TYR B:193 , LEU B:194 , GLU B:195
BINDING SITE FOR RESIDUE 1PE B 494
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3e9ia1 (A:4-145)
1b: SCOP_d3e9ib1 (B:4-145)
1c: SCOP_d3e9ic1 (C:4-145)
1d: SCOP_d3e9id1 (D:4-145)
2a: SCOP_d3e9ia2 (A:146-492)
2b: SCOP_d3e9ib2 (B:146-492)
2c: SCOP_d3e9ic2 (C:146-492)
2d: SCOP_d3e9id2 (D:146-492)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
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
d3e9ia1
A:4-145
1b
d3e9ib1
B:4-145
1c
d3e9ic1
C:4-145
1d
d3e9id1
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
d3e9ia2
A:146-492
2b
d3e9ib2
B:146-492
2c
d3e9ic2
C:146-492
2d
d3e9id2
D:146-492
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3e9iA02 (A:146-490)
1b: CATH_3e9iB02 (B:146-490)
1c: CATH_3e9iC02 (C:146-490)
1d: CATH_3e9iD02 (D:146-490)
2a: CATH_3e9iA01 (A:5-145)
2b: CATH_3e9iB01 (B:5-145)
2c: CATH_3e9iC01 (C:5-145)
2d: CATH_3e9iD01 (D:5-145)
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)
Organisms
(
)
(
)
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
3e9iA02
A:146-490
1b
3e9iB02
B:146-490
1c
3e9iC02
C:146-490
1d
3e9iD02
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
3e9iA01
A:5-145
2b
3e9iB01
B:5-145
2c
3e9iC01
C:5-145
2d
3e9iD01
D:5-145
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
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Show PDB file:
Asym.Unit (339 KB)
Header - Asym.Unit
Biol.Unit 1 (170 KB)
Header - Biol.Unit 1
Biol.Unit 2 (170 KB)
Header - Biol.Unit 2
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