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3FHJ
Asym. Unit
Info
Asym.Unit (294 KB)
Biol.Unit 1 (101 KB)
Biol.Unit 2 (98 KB)
Biol.Unit 3 (98 KB)
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(1)
Title
:
INDEPENDENT SATURATION OF THREE TRPRS SUBSITES GENERATES A PARTIALLY-ASSEMBLED STATE SIMILAR TO THOSE OBSERVED IN MOLECULAR SIMULATIONS
Authors
:
P. Laowanapiban, M. Kapustina, C. Vonrhein, M. Delarue, P. Koehl, C. W. Carter Jr.
Date
:
09 Dec 08 (Deposition) - 03 Feb 09 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: C,F (1x)
Keywords
:
Ligand-Dependent Domain Rearrangement, Mechanistic Pathway, Molecular Simulations, Aminoacyl-Trna Synthetase, Atp- Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis, Translation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Laowanapiban, M. Kapustina, C. Vonrhein, M. Delarue, P. Koehl, C. W. Carter
Independent Saturation Of Three Trprs Subsites Generates A Partially Assembled State Similar To Those Observed In Molecular Simulations.
Proc. Natl. Acad. Sci. Usa V. 106 1790 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 18)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
1c: ADENOSINE MONOPHOSPHATE (AMPc)
1d: ADENOSINE MONOPHOSPHATE (AMPd)
1e: ADENOSINE MONOPHOSPHATE (AMPe)
1f: ADENOSINE MONOPHOSPHATE (AMPf)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
3a: TRYPTOPHAN (TRPa)
3b: TRYPTOPHAN (TRPb)
3c: TRYPTOPHAN (TRPc)
3d: TRYPTOPHAN (TRPd)
3e: TRYPTOPHAN (TRPe)
3f: TRYPTOPHAN (TRPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
6
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
PO4
6
Ligand/Ion
PHOSPHATE ION
3
TRP
6
Mod. Amino Acid
TRYPTOPHAN
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:5 , GLY A:7 , GLN A:9 , VAL A:40 , HIS A:43 , MET A:129 , ASP A:132 , ILE A:133 , AMP A:1003
BINDING SITE FOR RESIDUE TRP A 1001
02
AC2
SOFTWARE
PHE D:5 , GLY D:7 , HIS D:43 , MET D:129 , ASP D:132 , GLN D:147 , AMP D:1003
BINDING SITE FOR RESIDUE TRP D 1001
03
AC3
SOFTWARE
PHE B:5 , GLY B:7 , VAL B:40 , HIS B:43 , MET B:129 , ASP B:132 , ILE B:133 , VAL B:141
BINDING SITE FOR RESIDUE TRP B 1001
04
AC4
SOFTWARE
PHE C:5 , GLY C:7 , GLN C:9 , VAL C:40 , HIS C:43 , MET C:129 , ASP C:132 , ILE C:133 , GLN C:147 , AMP C:1003
BINDING SITE FOR RESIDUE TRP C 1001
05
AC5
SOFTWARE
GLN E:9 , VAL E:40 , HIS E:43 , MET E:129 , ASP E:132 , ILE E:133 , GLN E:147 , AMP E:1003
BINDING SITE FOR RESIDUE TRP E 1001
06
AC6
SOFTWARE
PHE F:5 , GLY F:7 , VAL F:40 , HIS F:43 , MET F:129 , ASP F:132 , ILE F:133 , VAL F:141 , GLN F:147 , AMP F:1003
BINDING SITE FOR RESIDUE TRP F 1001
07
AC7
SOFTWARE
SER A:194 , LYS A:195 , AMP A:1003
BINDING SITE FOR RESIDUE PO4 A 1002
08
AC8
SOFTWARE
GLY A:17 , ASN A:18 , GLY A:21 , PRO A:142 , ASP A:146 , ILE A:176 , ALA A:181 , ILE A:183 , LYS A:192 , MET A:193 , TRP A:1001 , PO4 A:1002
BINDING SITE FOR RESIDUE AMP A 1003
09
AC9
SOFTWARE
ASN D:18 , LYS D:192 , SER D:194 , LYS D:195 , AMP D:1003
BINDING SITE FOR RESIDUE PO4 D 1002
10
BC1
SOFTWARE
GLY D:17 , ASN D:18 , ILE D:176 , ILE D:183 , LYS D:192 , MET D:193 , TRP D:1001 , PO4 D:1002
BINDING SITE FOR RESIDUE AMP D 1003
11
BC2
SOFTWARE
THR B:15 , ASN B:18 , SER B:194 , LYS B:195 , SER B:196 , AMP B:1003
BINDING SITE FOR RESIDUE PO4 B 1002
12
BC3
SOFTWARE
GLY B:17 , ASN B:18 , GLY B:21 , ILE B:183 , PO4 B:1002
BINDING SITE FOR RESIDUE AMP B 1003
13
BC4
SOFTWARE
MET C:193 , SER C:194 , LYS C:195 , SER C:196 , AMP C:1003
BINDING SITE FOR RESIDUE PO4 C 1002
14
BC5
SOFTWARE
GLY C:17 , ASN C:18 , GLY C:144 , ASP C:146 , ILE C:183 , LYS C:192 , MET C:193 , TRP C:1001 , PO4 C:1002
BINDING SITE FOR RESIDUE AMP C 1003
15
BC6
SOFTWARE
ASN E:18 , SER E:194 , LYS E:195 , AMP E:1003
BINDING SITE FOR RESIDUE PO4 E 1002
16
BC7
SOFTWARE
GLY E:17 , ASN E:18 , GLY E:21 , ALA E:22 , ILE E:183 , LYS E:192 , MET E:193 , TRP E:1001 , PO4 E:1002
BINDING SITE FOR RESIDUE AMP E 1003
17
BC8
SOFTWARE
ASN F:18 , LYS F:192 , SER F:194 , LYS F:195 , AMP F:1003
BINDING SITE FOR RESIDUE PO4 F 1002
18
BC9
SOFTWARE
GLY F:17 , ASN F:18 , GLY F:144 , ILE F:183 , LYS F:192 , MET F:193 , LYS F:195 , TRP F:1001 , PO4 F:1002
BINDING SITE FOR RESIDUE AMP F 1003
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: AA_TRNA_LIGASE_I (A:15-19,B:15-19,C:15-19,D:10-19,E:...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRNA_LIGASE_I
PS00178
Aminoacyl-transfer RNA synthetases class-I signature.
SYW_GEOSE
10-19
6
A:15-19
B:15-19
C:15-19
D:10-19
E:15-19
F:10-19
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3fhja_ (A:)
1b: SCOP_d3fhjb_ (B:)
1c: SCOP_d3fhjc_ (C:)
1d: SCOP_d3fhjd_ (D:)
1e: SCOP_d3fhje_ (E:)
1f: SCOP_d3fhjf_ (F:)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Nucleotidylyl transferase
(325)
Family
:
Class I aminoacyl-tRNA synthetases (RS), catalytic domain
(137)
Protein domain
:
Tryptophanyl-tRNA synthetase (TrpRS)
(28)
Bacillus stearothermophilus [TaxId: 1422]
(11)
1a
d3fhja_
A:
1b
d3fhjb_
B:
1c
d3fhjc_
C:
1d
d3fhjd_
D:
1e
d3fhje_
E:
1f
d3fhjf_
F:
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_3fhjD01 (D:1-182,D:294-326)
1b: CATH_3fhjA01 (A:1-182,A:294-326)
1c: CATH_3fhjC01 (C:1-182,C:294-326)
1d: CATH_3fhjE01 (E:1-182,E:294-326)
1e: CATH_3fhjF01 (F:1-182,F:294-326)
1f: CATH_3fhjB01 (B:1-182,B:294-326)
2a: CATH_3fhjA02 (A:183-293)
2b: CATH_3fhjB02 (B:183-293)
2c: CATH_3fhjF02 (F:183-293)
2d: CATH_3fhjE02 (E:183-293)
2e: CATH_3fhjD02 (D:183-293)
2f: CATH_3fhjC02 (C:183-293)
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(
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Bacillus stearothermophilus. Organism_taxid: 1422. Strain: nc1500.
(1)
1a
3fhjD01
D:1-182,D:294-326
1b
3fhjA01
A:1-182,A:294-326
1c
3fhjC01
C:1-182,C:294-326
1d
3fhjE01
E:1-182,E:294-326
1e
3fhjF01
F:1-182,F:294-326
1f
3fhjB01
B:1-182,B:294-326
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Tyrosyl-Transfer RNA Synthetase
(70)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase
(70)
Bacillus stearothermophilus. Organism_taxid: 1422. Strain: nc1500.
(1)
2a
3fhjA02
A:183-293
2b
3fhjB02
B:183-293
2c
3fhjF02
F:183-293
2d
3fhjE02
E:183-293
2e
3fhjD02
D:183-293
2f
3fhjC02
C:183-293
[
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Pfam Domains
(0, 0)
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all PFAM domains
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