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1KJ9
Asym. Unit
Info
Asym.Unit (149 KB)
Biol.Unit 1 (142 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PURT-ENCODED GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE COMPLEXED WITH MG-ATP
Authors
:
J. B. Thoden, S. M. Firestine, S. J. Benkovic, H. M. Holden
Date
:
04 Dec 01 (Deposition) - 28 Jun 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Atp-Grasp, Purine Biosynthesis, Nucleotide, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. B. Thoden, S. M. Firestine, S. J. Benkovic, H. M. Holden
Purt-Encoded Glycinamide Ribonucleotide Transformylase. Accommodation Of Adenosine Nucleotide Analogs Within The Active Site.
J. Biol. Chem. V. 277 23898 2002
(for further references see the
PDB file header
)
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Hetero Components
(6, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
5a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
4
MG
5
Ligand/Ion
MAGNESIUM ION
5
MPO
1
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
6
NA
2
Ligand/Ion
SODIUM ION
[
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ATP A:1 , GLU A:279 , EDO A:403 , HOH A:417
BINDING SITE FOR RESIDUE MG A 393
02
AC2
SOFTWARE
ATP A:1 , GLU A:267 , GLU A:279 , HOH A:419
BINDING SITE FOR RESIDUE MG A 394
03
AC3
SOFTWARE
ATP A:1 , ASP A:286 , HOH A:474 , HOH A:478 , HOH A:482 , HOH A:549
BINDING SITE FOR RESIDUE MG A 395
04
AC4
SOFTWARE
GLU B:279 , ATP B:395 , HOH B:447 , HOH B:502
BINDING SITE FOR RESIDUE MG B 393
05
AC5
SOFTWARE
GLU B:267 , GLU B:279 , ATP B:395 , HOH B:557
BINDING SITE FOR RESIDUE MG B 394
06
AC6
SOFTWARE
ALA A:53 , HOH A:483 , HOH A:779 , ALA B:53 , HOH B:465 , HOH B:647 , HOH B:649
BINDING SITE FOR RESIDUE NA A 396
07
AC7
SOFTWARE
ASN A:100 , VAL A:101 , PRO A:103 , HOH A:438
BINDING SITE FOR RESIDUE NA A 397
08
AC8
SOFTWARE
ARG A:43 , ARG A:119 , PHE A:134 , HOH A:571
BINDING SITE FOR RESIDUE CL A 398
09
AC9
SOFTWARE
GLU A:84
BINDING SITE FOR RESIDUE CL A 399
10
BC1
SOFTWARE
ARG A:114 , ILE A:153 , LYS A:155 , SER A:160 , SER A:161 , GLY A:162 , GLN A:165 , GLU A:195 , GLY A:196 , VAL A:198 , PHE A:200 , GLU A:203 , GLN A:225 , GLY A:228 , GLU A:267 , PHE A:269 , GLU A:279 , MG A:393 , MG A:394 , MG A:395 , EDO A:403 , HOH A:417 , HOH A:419 , HOH A:428 , HOH A:434 , HOH A:474 , HOH A:478 , HOH A:482 , HOH A:505 , HOH A:521 , HOH A:526 , HOH A:549
BINDING SITE FOR RESIDUE ATP A 1
11
BC2
SOFTWARE
ARG B:114 , LYS B:155 , SER B:159 , SER B:160 , SER B:161 , GLY B:162 , GLN B:165 , GLU B:195 , GLY B:196 , VAL B:198 , PHE B:200 , GLU B:203 , GLU B:267 , PHE B:269 , GLU B:279 , MG B:393 , MG B:394 , HOH B:447 , HOH B:502 , HOH B:516 , HOH B:557 , HOH B:613 , HOH B:684 , HOH B:797
BINDING SITE FOR RESIDUE ATP B 395
12
BC3
SOFTWARE
ASP A:46 , MET A:50 , HIS A:51 , ARG A:55 , SER A:56 , GLU A:143 , HOH A:415 , HOH A:483 , HOH A:552 , HOH A:865 , LEU B:8 , HIS B:54
BINDING SITE FOR RESIDUE MPO A 400
13
BC4
SOFTWARE
ARG A:9 , ALA A:12 , ARG A:14 , GLU A:37 , HOH A:847
BINDING SITE FOR RESIDUE EDO A 401
14
BC5
SOFTWARE
ILE A:148 , TYR A:150 , PRO A:151 , GLY A:196 , VAL A:197 , HOH A:587
BINDING SITE FOR RESIDUE EDO A 402
15
BC6
SOFTWARE
ATP A:1 , GLU A:84 , GLU A:267 , GLU A:279 , SER A:281 , HIS A:285 , MG A:393 , HOH A:417 , HOH A:434
BINDING SITE FOR RESIDUE EDO A 403
16
BC7
SOFTWARE
LEU A:256 , GLY A:259 , GLY A:260 , TYR A:261 , HOH A:412 , HOH A:479
BINDING SITE FOR RESIDUE EDO A 404
17
BC8
SOFTWARE
PRO A:10
BINDING SITE FOR RESIDUE EDO A 405
18
BC9
SOFTWARE
LEU B:242
BINDING SITE FOR RESIDUE EDO B 396
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
All Exons
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1kj9a1 (A:319-392)
1b: SCOP_d1kj9b1 (B:319-392)
2a: SCOP_d1kj9a3 (A:113-318)
2b: SCOP_d1kj9b3 (B:113-318)
3a: SCOP_d1kj9a2 (A:2-112)
3b: SCOP_d1kj9b2 (B:2-112)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Rudiment single hybrid motif
(69)
Family
:
BC C-terminal domain-like
(40)
Protein domain
:
Glycinamide ribonucleotide transformylase PurT, C-domain
(7)
Escherichia coli [TaxId: 562]
(7)
1a
d1kj9a1
A:319-392
1b
d1kj9b1
B:319-392
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
BC ATP-binding domain-like
(53)
Protein domain
:
Glycinamide ribonucleotide transformylase PurT, domain 2
(7)
Escherichia coli [TaxId: 562]
(7)
2a
d1kj9a3
A:113-318
2b
d1kj9b3
B:113-318
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
BC N-terminal domain-like
(50)
Protein domain
:
Glycinamide ribonucleotide transformylase PurT, N-domain
(7)
Escherichia coli [TaxId: 562]
(7)
3a
d1kj9a2
A:2-112
3b
d1kj9b2
B:2-112
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1kj9A03 (A:197-391)
1b: CATH_1kj9B03 (B:197-391)
2a: CATH_1kj9B02 (B:123-196)
2b: CATH_1kj9A02 (A:123-196)
3a: CATH_1kj9A01 (A:2-122)
3b: CATH_1kj9B01 (B:2-122)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
ATP-grasp fold, B domain
(118)
Escherichia coli. Organism_taxid: 562.
(17)
1a
1kj9A03
A:197-391
1b
1kj9B03
B:197-391
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Escherichia coli. Organism_taxid: 562.
(15)
2a
1kj9B02
B:123-196
2b
1kj9A02
A:123-196
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.20, no name defined]
(85)
Escherichia coli. Organism_taxid: 562.
(10)
3a
1kj9A01
A:2-122
3b
1kj9B01
B:2-122
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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