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1JJC
Asym. Unit
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Asym.Unit (181 KB)
Biol.Unit 1 (345 KB)
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(1)
Title
:
CRYSTAL STRUCTURE AT 2.6A RESOLUTION OF PHENYLALANYL-TRNA SYNTHETASE COMPLEXED WITH PHENYLALANYL-ADENYLATE IN THE PRESENCE OF MANGANESE
Authors
:
M. G. Safro, R. Fishman, N. Moor, V. Ankilova
Date
:
04 Jul 01 (Deposition) - 02 Nov 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Heterodimer, Phenylalanyl-Trna, Thermus Thermophilus, Ligase
(Keyword Search:
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)
Reference
:
R. Fishman, V. Ankilova, N. Moor, M. Safro
Structure At 2. 6 A Resolution Of Phenylalanyl-Trna Synthetase Complexed With Phenylalanyl-Adenylate In The Presence Of Manganese.
Acta Crystallogr. , Sect. D V. 57 1534 2001
(for further references see the
PDB file header
)
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: ADENOSINE-5'-[PHENYLALANINYL-PHOSP... (FA5a)
2a: MANGANESE (II) ION (MNa)
3a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FA5
1
Ligand/Ion
ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE]
2
MN
1
Ligand/Ion
MANGANESE (II) ION
3
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:262 , GLU B:461 , HOH B:903
BINDING SITE FOR RESIDUE MN B 901
2
AC2
SOFTWARE
ARG B:407 , TYR B:410 , ARG B:413
BINDING SITE FOR RESIDUE SO4 B 902
3
AC3
SOFTWARE
TRP A:149 , HIS A:178 , SER A:180 , ARG A:204 , GLU A:206 , GLU A:213 , GLN A:218 , GLU A:220 , PHE A:258 , PHE A:260 , LEU A:280 , GLY A:281 , GLY A:282 , ALA A:283 , ALA A:314 , PHE A:315 , GLY A:316 , GLY A:318 , HOH A:1002 , HOH A:1040 , HOH A:1064
BINDING SITE FOR RESIDUE FA5 A 999
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRBD (B:39-147)
2: B5 (B:399-474)
3: FDX_ACB (B:688-780)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRBD
PS50886
tRNA-binding domain profile.
SYFB_THET8
39-147
1
B:39-147
2
B5
PS51483
B5 domain profile.
SYFB_THET8
399-474
1
B:399-474
3
FDX_ACB
PS51447
Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.
SYFB_THET8
688-780
1
B:688-780
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(6, 7)
Info
All SCOP Domains
1a: SCOP_d1jjcb1 (B:1-38,B:152-190)
1b: SCOP_d1jjcb2 (B:400-474)
2a: SCOP_d1jjcb3 (B:39-151)
3a: SCOP_d1jjcb6 (B:191-399)
4a: SCOP_d1jjca_ (A:)
5a: SCOP_d1jjcb5 (B:475-681)
6a: SCOP_d1jjcb4 (B:682-785)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Putative DNA-binding domain
(45)
Superfamily
:
Putative DNA-binding domain
(45)
Family
:
Domains B1 and B5 of PheRS-beta, PheT
(11)
Protein domain
:
Domains B1 and B5 of PheRS-beta, PheT
(11)
Thermus thermophilus [TaxId: 274]
(11)
1a
d1jjcb1
B:1-38,B:152-190
1b
d1jjcb2
B:400-474
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Myf domain
(20)
Protein domain
:
Domain B2 of PheRS-beta, PheT
(11)
Thermus thermophilus [TaxId: 274]
(11)
2a
d1jjcb3
B:39-151
Fold
:
PheT/TilS domain
(12)
Superfamily
:
PheT/TilS domain
(12)
Family
:
B3/B4 domain of PheRS, PheT
(11)
Protein domain
:
B3/B4 domain of PheRS, PheT
(11)
Thermus thermophilus [TaxId: 274]
(11)
3a
d1jjcb6
B:191-399
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
:
Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS
(11)
Thermus thermophilus [TaxId: 274]
(11)
4a
d1jjca_
A:
Protein domain
:
Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain
(11)
Thermus thermophilus [TaxId: 274]
(11)
5a
d1jjcb5
B:475-681
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Anticodon-binding domain of PheRS
(11)
Family
:
Anticodon-binding domain of PheRS
(11)
Protein domain
:
Phenylalanyl-tRNA synthetase
(11)
Thermus thermophilus [TaxId: 274]
(11)
6a
d1jjcb4
B:682-785
[
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CATH Domains
(6, 7)
Info
all CATH domains
1a: CATH_1jjcB06 (B:690-785)
2a: CATH_1jjcA00 (A:85-350)
2b: CATH_1jjcB05 (B:489-679)
3a: CATH_1jjcB01 (B:1-37,B:154-186)
4a: CATH_1jjcB04 (B:401-474)
5a: CATH_1jjcB03 (B:187-400)
6a: CATH_1jjcB02 (B:38-153)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.380, no name defined]
(12)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
1a
1jjcB06
B:690-785
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
2a
1jjcA00
A:85-350
2b
1jjcB05
B:489-679
Topology
:
Phenylalanyl-tRNA Synthetase; Chain B, domain 1
(22)
Homologous Superfamily
:
[code=3.30.56.10, no name defined]
(12)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
3a
1jjcB01
B:1-37,B:154-186
Homologous Superfamily
:
[code=3.30.56.20, no name defined]
(12)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
4a
1jjcB04
B:401-474
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
Phenylalanyl-tRNA Synthetase; Chain B, domain 3
(12)
Homologous Superfamily
:
Phenylalanyl-trna Synthetase, Chain B, domain 3
(12)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
5a
1jjcB03
B:187-400
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
6a
1jjcB02
B:38-153
[
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Pfam Domains
(5, 6)
Info
all PFAM domains
1a: PFAM_tRNA_bind_1jjcB01 (B:45-145)
2a: PFAM_B3_4_1jjcB02 (B:209-385)
3a: PFAM_B5_1jjcB03 (B:401-469)
4a: PFAM_FDX_ACB_1jjcB04 (B:688-780)
5a: PFAM_tRNA_synt_2d_1jjcA01 (A:85-346)
5b: PFAM_tRNA_synt_2d_1jjcB05 (B:485-671)
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Clans
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)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
OB
(224)
Family
:
tRNA_bind
(10)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
1a
tRNA_bind-1jjcB01
B:45-145
Clan
:
PheT-TilS
(7)
Family
:
B3_4
(6)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
2a
B3_4-1jjcB02
B:209-385
Clan
:
no clan defined [family: B5]
(6)
Family
:
B5
(6)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
3a
B5-1jjcB03
B:401-469
Clan
:
no clan defined [family: FDX-ACB]
(5)
Family
:
FDX-ACB
(5)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
4a
FDX-ACB-1jjcB04
B:688-780
Clan
:
tRNA_synt_II
(64)
Family
:
tRNA-synt_2d
(5)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
5a
tRNA-synt_2d-1jjcA01
A:85-346
5b
tRNA-synt_2d-1jjcB05
B:485-671
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