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3E9I
Asym. Unit
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
(3, 12)
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
4
Ligand/Ion
PENTAETHYLENE GLYCOL
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
XAH
4
Ligand/Ion
5'-O-{(R)-HYDROXY[(L-LYSYLAMINO)OXY]PHOSPHORYL}ADENOSINE
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:404 , GLU A:411 , ASN A:414 , XAH A:1001
BINDING SITE FOR RESIDUE MG A 1000
02
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
03
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
04
AC4
SOFTWARE
GLU B:404 , GLU B:411 , ASN B:414 , XAH B:1101
BINDING SITE FOR RESIDUE MG B 1100
05
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
06
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
07
AC7
SOFTWARE
GLU C:404 , GLU C:411 , ASN C:414 , XAH C:1201
BINDING SITE FOR RESIDUE MG C 1200
08
AC8
SOFTWARE
GLY C:207 , ALA C:208 , GLU C:231 , ARG C:253 , ARG C:260 , HIS C:261 , ASN C:262 , PHE C:265 , MET C:267 , GLU C:269 , TYR C:271 , GLU C:411 , HIS C:412 , ALA C:413 , ASN C:414 , PHE C:416 , GLU C:418 , GLY C:465 , GLY C:467 , ARG C:470 , ILE C:481 , HOH C:780 , HOH C:788 , HOH C:925 , MG C:1200
BINDING SITE FOR RESIDUE XAH C 1201
09
AC9
SOFTWARE
LEU C:179 , GLN C:182 , ARG C:186 , GLU C:294 , ASP D:189 , SER D:190 , TYR D:193 , LEU D:194 , GLU D:195 , HOH D:930
BINDING SITE FOR RESIDUE 1PE C 494
10
BC1
SOFTWARE
ARG C:186 , ASP C:189 , SER C:190 , TYR C:193 , LEU C:194 , GLU C:195 , GLN D:182
BINDING SITE FOR RESIDUE 1PE C 1202
11
BC2
SOFTWARE
GLU D:404 , GLU D:411 , ASN D:414 , XAH D:1301
BINDING SITE FOR RESIDUE MG D 1300
12
BC3
SOFTWARE
GLY D:207 , ALA D:208 , ALA D:229 , GLU D:231 , ARG D:253 , GLU D:255 , ARG D:260 , HIS D:261 , ASN D:262 , PHE D:265 , GLU D:269 , TYR D:271 , GLU D:411 , HIS D:412 , ASN D:414 , PHE D:416 , GLU D:418 , GLY D:467 , ARG D:470 , ILE D:481 , HOH D:870 , MG D:1300
BINDING SITE FOR RESIDUE XAH D 1301
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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
(
)
(
)
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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all PFAM domains
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Chain D
Asymmetric Unit 1
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Asym.Unit (339 KB)
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