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3BJU
Biol. Unit 1
Info
Asym.Unit (357 KB)
Biol.Unit 1 (349 KB)
Biol.Unit 2 (177 KB)
Biol.Unit 3 (178 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TETRAMERIC FORM OF HUMAN LYSYL-TRNA SYNTHETASE
Authors
:
M. Guo, X. L. Yang, P. Schimmel
Date
:
04 Dec 07 (Deposition) - 05 Feb 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.31
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Trna Synthetase, Lysyl-Trna, Aminoacyl-Trna Synthetase, Atp- Binding, Cytoplasm, Ligase, Nucleotide-Binding, Phosphoprotein, Polymorphism, Protein Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Guo, M. Ignatov, K. Musier-Forsyth, P. Schimmel, X. L. Yang
Crystal Structure Of Tetrameric Form Of Human Lysyl-Trna Synthetase: Implications For Multisynthetase Complex Formation
Proc. Natl. Acad. Sci. Usa V. 105 2331 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
2k: CALCIUM ION (CAk)
2l: CALCIUM ION (CAl)
3a: LYSINE (LYSa)
3b: LYSINE (LYSb)
3c: LYSINE (LYSc)
3d: LYSINE (LYSd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
4
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
LYS
4
Mod. Amino Acid
LYSINE
[
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]
Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC9 (SOFTWARE)
07: AD1 (SOFTWARE)
08: AD2 (SOFTWARE)
09: AD3 (SOFTWARE)
10: AD4 (SOFTWARE)
11: BC1 (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
GLU A:487 , GLU A:494 , ATP A:603 , CA A:608 , HOH A:786 , HOH A:794
BINDING SITE FOR RESIDUE CA A 606
02
AC3
SOFTWARE
ATP A:603 , HOH A:653 , HOH A:714
BINDING SITE FOR RESIDUE CA A 607
03
AC4
SOFTWARE
GLU A:494 , ATP A:603 , CA A:606 , HOH A:674 , HOH A:786 , HOH A:824
BINDING SITE FOR RESIDUE CA A 608
04
AC6
SOFTWARE
GLU B:487 , GLU B:494 , ATP B:603 , CA B:608 , HOH B:812 , HOH B:866
BINDING SITE FOR RESIDUE CA B 606
05
AC7
SOFTWARE
ATP B:603 , HOH B:827 , HOH B:903 , HOH B:914
BINDING SITE FOR RESIDUE CA B 607
06
AC9
SOFTWARE
GLU B:494 , ATP B:603 , CA B:606 , HOH B:812 , HOH B:840 , HOH B:843
BINDING SITE FOR RESIDUE CA B 608
07
AD1
SOFTWARE
GLU C:487 , GLU C:494 , ATP C:603 , CA C:608
BINDING SITE FOR RESIDUE CA C 606
08
AD2
SOFTWARE
ATP C:603 , HOH C:704 , HOH C:856
BINDING SITE FOR RESIDUE CA C 607
09
AD3
SOFTWARE
GLU C:494 , ATP C:603 , CA C:606 , HOH C:670 , HOH C:838
BINDING SITE FOR RESIDUE CA C 608
10
AD4
SOFTWARE
ATP D:603 , HOH D:752
BINDING SITE FOR RESIDUE CA D 607
11
BC1
SOFTWARE
GLU D:487 , GLU D:494 , ATP D:603 , CA D:608
BINDING SITE FOR RESIDUE CA D 606
12
BC3
SOFTWARE
GLU D:494 , ATP D:603 , CA D:606 , HOH D:699 , HOH D:759 , HOH D:770
BINDING SITE FOR RESIDUE CA D 608
13
BC4
SOFTWARE
GLY A:277 , ALA A:278 , ALA A:299 , GLU A:301 , ARG A:323 , GLU A:339 , TYR A:341 , ASN A:497 , TYR A:499 , GLU A:501 , GLY A:546 , ATP A:603 , HOH A:698
BINDING SITE FOR RESIDUE LYS A 601
14
BC5
SOFTWARE
ARG A:323 , GLU A:325 , THR A:330 , HIS A:331 , ASN A:332 , PHE A:335 , GLU A:494 , ILE A:495 , ASN A:497 , GLY A:550 , ARG A:553 , ILE A:564 , LYS A:601 , CA A:606 , CA A:607 , CA A:608 , HOH A:609 , HOH A:653 , HOH A:674 , HOH A:776 , HOH A:786 , HOH A:824 , HOH A:825
BINDING SITE FOR RESIDUE ATP A 603
15
BC6
SOFTWARE
GLY B:277 , ALA B:278 , ALA B:299 , GLU B:301 , ARG B:323 , GLU B:339 , TYR B:341 , ASN B:497 , TYR B:499 , GLU B:501 , GLY B:546 , ATP B:603 , HOH B:790
BINDING SITE FOR RESIDUE LYS B 601
16
BC7
SOFTWARE
ARG B:323 , GLU B:325 , THR B:330 , HIS B:331 , ASN B:332 , PHE B:335 , GLU B:494 , ILE B:495 , ASN B:497 , GLY B:550 , ARG B:553 , LYS B:601 , CA B:606 , CA B:607 , CA B:608 , HOH B:678 , HOH B:740 , HOH B:812 , HOH B:827 , HOH B:843 , HOH B:875 , HOH B:914
BINDING SITE FOR RESIDUE ATP B 603
17
BC8
SOFTWARE
GLY C:277 , ALA C:278 , ALA C:299 , GLU C:301 , ARG C:323 , GLU C:339 , TYR C:341 , ASN C:497 , TYR C:499 , GLU C:501 , GLY C:546 , ATP C:603 , HOH C:714
BINDING SITE FOR RESIDUE LYS C 601
18
BC9
SOFTWARE
ARG C:323 , GLU C:325 , THR C:330 , HIS C:331 , ASN C:332 , PHE C:335 , GLU C:494 , ILE C:495 , ASN C:497 , GLY C:550 , ARG C:553 , ILE C:564 , LYS C:601 , CA C:606 , CA C:607 , CA C:608 , HOH C:609 , HOH C:670 , HOH C:678 , HOH C:797 , HOH C:856
BINDING SITE FOR RESIDUE ATP C 603
19
CC1
SOFTWARE
GLY D:277 , ALA D:278 , ALA D:299 , GLU D:301 , GLU D:339 , TYR D:341 , ASN D:497 , TYR D:499 , GLU D:501 , GLY D:546 , GLY D:548 , ATP D:603 , HOH D:689
BINDING SITE FOR RESIDUE LYS D 601
20
CC2
SOFTWARE
ARG D:323 , GLU D:325 , THR D:330 , HIS D:331 , ASN D:332 , PHE D:335 , GLU D:494 , ILE D:495 , ASN D:497 , GLY D:550 , ARG D:553 , LYS D:601 , CA D:606 , CA D:607 , CA D:608 , HOH D:610 , HOH D:687 , HOH D:699 , HOH D:752 , HOH D:759 , HOH D:797
BINDING SITE FOR RESIDUE ATP D 603
[
close Site info
]
SAPs(SNPs)/Variants
(5, 20)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_064911 (L105H, chain A/B/C/D, )
2: VAR_070233 (Y145H, chain A/B/C/D, )
3: VAR_052640 (G179A, chain A/B/C/D, )
4: VAR_064912 (I274M, chain A/B/C/D, )
5: VAR_070234 (D349N, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_064911
L
105
H
SYK_HUMAN
Disease (CMTRIB)
---
A/B/C/D
L
105
H
2
UniProt
VAR_070233
Y
145
H
SYK_HUMAN
Disease (DFNB89)
---
A/B/C/D
Y
145
H
3
UniProt
VAR_052640
G
179
A
SYK_HUMAN
Polymorphism
11557665
A/B/C/D
G
179
A
4
UniProt
VAR_064912
I
274
M
SYK_HUMAN
Disease (CMTRIB)
---
A/B/C/D
I
274
M
5
UniProt
VAR_070234
D
349
N
SYK_HUMAN
Disease (DFNB89)
---
A/B/C/D
D
349
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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_d3bjua1 (A:70-221)
1b: SCOP_d3bjub1 (B:72-214)
1c: SCOP_d3bjuc1 (C:72-221)
1d: SCOP_d3bjud1 (D:71-221)
2a: SCOP_d3bjua2 (A:222-576)
2b: SCOP_d3bjub2 (B:223-574)
2c: SCOP_d3bjuc2 (C:222-575)
2d: SCOP_d3bjud2 (D:222-575)
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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)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d3bjua1
A:70-221
1b
d3bjub1
B:72-214
1c
d3bjuc1
C:72-221
1d
d3bjud1
D:71-221
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)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d3bjua2
A:222-576
2b
d3bjub2
B:223-574
2c
d3bjuc2
C:222-575
2d
d3bjud2
D:222-575
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3bjuB02 (B:223-573)
1b: CATH_3bjuA02 (A:221-573)
1c: CATH_3bjuC02 (C:221-573)
1d: CATH_3bjuD02 (D:221-573)
2a: CATH_3bjuB01 (B:73-214)
2b: CATH_3bjuD01 (D:73-214)
2c: CATH_3bjuA01 (A:73-220)
2d: CATH_3bjuC01 (C:73-220)
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(
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(
)
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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)
Human (Homo sapiens)
(11)
1a
3bjuB02
B:223-573
1b
3bjuA02
A:221-573
1c
3bjuC02
C:221-573
1d
3bjuD02
D:221-573
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Human (Homo sapiens)
(27)
2a
3bjuB01
B:73-214
2b
3bjuD01
D:73-214
2c
3bjuA01
A:73-220
2d
3bjuC01
C:73-220
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Chain D
Asymmetric Unit 1
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Asym.Unit (357 KB)
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