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3A74
Asym. Unit
Info
Asym.Unit (349 KB)
Biol.Unit 1 (174 KB)
Biol.Unit 2 (173 KB)
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(1)
Title
:
LYSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH DIADENOSINE TETRAPHOSPHATE (AP4A)
Authors
:
H. Sakurama, T. Takita, B. Mikami, T. Itoh, K. Yasukawa, K. Inouye
Date
:
13 Sep 09 (Deposition) - 22 Sep 10 (Release) - 22 Sep 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
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, Magnesium, Metal-Binding, Nucleotide- Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
H. Sakurama, T. Takita, B. Mikami, T. Itoh, K. Yasukawa, K. Inouye
Crystal Structure Of Lysyl-Trna Synthetase From Bacillus Stearothermophilus In Complex With Diadenosine Tetraphosphate (Ap4A): Insights Into Ap4A Synthesis Mechanisms And Implication For Recognition Of Discriminator Base Of Trna^Lys
To Be Published
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Hetero Components
(3, 20)
Info
All Hetero Components
1a: BIS(ADENOSINE)-5'-TETRAPHOSPHATE (B4Pa)
1b: BIS(ADENOSINE)-5'-TETRAPHOSPHATE (B4Pb)
1c: BIS(ADENOSINE)-5'-TETRAPHOSPHATE (B4Pc)
1d: BIS(ADENOSINE)-5'-TETRAPHOSPHATE (B4Pd)
2a: 2,6-DIAMINO-HEXANOIC ACID AMIDE (LYNa)
2b: 2,6-DIAMINO-HEXANOIC ACID AMIDE (LYNb)
2c: 2,6-DIAMINO-HEXANOIC ACID AMIDE (LYNc)
2d: 2,6-DIAMINO-HEXANOIC ACID AMIDE (LYNd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B4P
4
Ligand/Ion
BIS(ADENOSINE)-5'-TETRAPHOSPHATE
2
LYN
4
Ligand/Ion
2,6-DIAMINO-HEXANOIC ACID AMIDE
3
MG
12
Ligand/Ion
MAGNESIUM ION
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Sites
(20, 20)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:253 , GLU A:255 , GLY A:256 , SER A:258 , ARG A:260 , HIS A:261 , ASN A:262 , PHE A:265 , MET A:267 , GLU A:366 , GLU A:370 , GLU A:411 , HIS A:412 , ASN A:414 , GLY A:467 , ARG A:470 , ILE A:481 , LYN A:495 , HOH A:508 , HOH A:511 , HOH A:543 , HOH A:747 , HOH A:802 , HOH A:885 , HOH A:914 , MG A:1000 , MG A:1001 , MG A:1002 , HOH A:1291 , HOH A:1300
BINDING SITE FOR RESIDUE B4P A 494
02
AC2
SOFTWARE
GLY A:207 , ALA A:229 , GLU A:231 , ARG A:253 , MET A:267 , GLU A:269 , TYR A:271 , ASN A:414 , PHE A:416 , GLU A:418 , B4P A:494
BINDING SITE FOR RESIDUE LYN A 495
03
AC3
SOFTWARE
GLU A:404 , GLU A:411 , ALA A:413 , ASN A:414 , B4P A:494
BINDING SITE FOR RESIDUE MG A 1000
04
AC4
SOFTWARE
B4P A:494 , HOH A:508 , HOH A:543 , HOH A:802 , HOH A:1291
BINDING SITE FOR RESIDUE MG A 1001
05
AC5
SOFTWARE
GLU A:404 , GLU A:411 , B4P A:494 , HOH A:1300
BINDING SITE FOR RESIDUE MG A 1002
06
AC6
SOFTWARE
ARG B:253 , GLU B:255 , GLY B:256 , SER B:258 , ARG B:260 , HIS B:261 , ASN B:262 , PHE B:265 , MET B:267 , GLU B:366 , GLU B:370 , GLU B:411 , HIS B:412 , ALA B:413 , ASN B:414 , GLY B:467 , ARG B:470 , ILE B:481 , LYN B:495 , HOH B:502 , HOH B:580 , HOH B:864 , HOH B:866 , HOH B:868 , HOH B:870 , MG B:1100 , MG B:1101 , MG B:1102 , HOH B:1206 , GLN C:438
BINDING SITE FOR RESIDUE B4P B 494
07
AC7
SOFTWARE
GLY B:207 , ALA B:208 , GLU B:231 , ARG B:253 , MET B:267 , GLU B:269 , TYR B:271 , ASN B:414 , PHE B:416 , GLU B:418 , B4P B:494
BINDING SITE FOR RESIDUE LYN B 495
08
AC8
SOFTWARE
GLU B:404 , GLU B:411 , ASN B:414 , B4P B:494 , HOH B:1206
BINDING SITE FOR RESIDUE MG B 1100
09
AC9
SOFTWARE
B4P B:494 , HOH B:580 , HOH B:864 , HOH B:865 , HOH B:868
BINDING SITE FOR RESIDUE MG B 1101
10
BC1
SOFTWARE
GLU B:404 , GLU B:411 , B4P B:494 , HOH B:1206
BINDING SITE FOR RESIDUE MG B 1102
11
BC2
SOFTWARE
ARG C:253 , GLU C:255 , GLY C:256 , SER C:258 , ARG C:260 , HIS C:261 , ASN C:262 , PHE C:265 , MET C:267 , GLU C:366 , GLU C:370 , GLU C:411 , HIS C:412 , ASN C:414 , GLY C:467 , ARG C:470 , ILE C:481 , LYN C:495 , HOH C:507 , HOH C:509 , HOH C:723 , HOH C:819 , HOH C:915 , HOH C:917 , HOH C:925 , MG C:1200 , MG C:1201 , MG C:1202 , HOH C:1302 , HOH C:1303 , HOH C:1304
BINDING SITE FOR RESIDUE B4P C 494
12
BC3
SOFTWARE
GLY C:207 , ALA C:229 , GLU C:231 , ARG C:253 , MET C:267 , GLU C:269 , TYR C:271 , ASN C:414 , PHE C:416 , GLU C:418 , B4P C:494
BINDING SITE FOR RESIDUE LYN C 495
13
BC4
SOFTWARE
GLU C:404 , GLU C:411 , ALA C:413 , ASN C:414 , B4P C:494
BINDING SITE FOR RESIDUE MG C 1200
14
BC5
SOFTWARE
B4P C:494 , HOH C:509 , HOH C:819 , HOH C:915 , HOH C:917
BINDING SITE FOR RESIDUE MG C 1201
15
BC6
SOFTWARE
GLU C:404 , GLU C:411 , B4P C:494 , HOH C:1302
BINDING SITE FOR RESIDUE MG C 1202
16
BC7
SOFTWARE
GLN A:438 , ARG D:253 , GLU D:255 , GLY D:256 , ARG D:260 , HIS D:261 , ASN D:262 , PHE D:265 , MET D:267 , GLU D:366 , GLU D:370 , GLU D:411 , HIS D:412 , ALA D:413 , ASN D:414 , GLY D:467 , ARG D:470 , ILE D:481 , LYN D:495 , HOH D:501 , HOH D:596 , HOH D:851 , HOH D:853 , HOH D:855 , HOH D:1164 , MG D:1300 , MG D:1301 , MG D:1302 , HOH D:1307
BINDING SITE FOR RESIDUE B4P D 494
17
BC8
SOFTWARE
GLY D:207 , ALA D:208 , GLU D:231 , ARG D:253 , MET D:267 , GLU D:269 , TYR D:271 , ASN D:414 , PHE D:416 , GLU D:418 , B4P D:494
BINDING SITE FOR RESIDUE LYN D 495
18
BC9
SOFTWARE
GLU D:404 , GLU D:411 , ALA D:413 , ASN D:414 , B4P D:494 , HOH D:1305
BINDING SITE FOR RESIDUE MG D 1300
19
CC1
SOFTWARE
B4P D:494 , HOH D:596 , HOH D:851 , HOH D:852 , HOH D:853
BINDING SITE FOR RESIDUE MG D 1301
20
CC2
SOFTWARE
GLU D:404 , GLU D:411 , B4P D:494 , HOH D:1307
BINDING SITE FOR RESIDUE MG D 1302
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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_d3a74a1 (A:4-145)
1b: SCOP_d3a74b1 (B:4-145)
1c: SCOP_d3a74c1 (C:4-145)
1d: SCOP_d3a74d1 (D:4-145)
2a: SCOP_d3a74a2 (A:146-492)
2b: SCOP_d3a74b2 (B:146-492)
2c: SCOP_d3a74c2 (C:146-492)
2d: SCOP_d3a74d2 (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
:
Anticodon-binding domain
(21)
Protein domain
:
Lysyl-tRNA synthetase (LysRS)
(10)
Geobacillus stearothermophilus [TaxId: 1422]
(1)
1a
d3a74a1
A:4-145
1b
d3a74b1
B:4-145
1c
d3a74c1
C:4-145
1d
d3a74d1
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
:
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
(103)
Protein domain
:
Lysyl-tRNA synthetase (LysRS)
(8)
Geobacillus stearothermophilus [TaxId: 1422]
(1)
2a
d3a74a2
A:146-492
2b
d3a74b2
B:146-492
2c
d3a74c2
C:146-492
2d
d3a74d2
D:146-492
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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