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1KJ8
Biol. Unit 1
Info
Asym.Unit (147 KB)
Biol.Unit 1 (140 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PURT-ENCODED GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE IN COMPLEX WITH MG-ATP AND GAR
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
(4, 8)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
4a: GLYCINAMIDE RIBONUCLEOTIDE (GARa)
4b: GLYCINAMIDE RIBONUCLEOTIDE (GARb)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
6a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
7a: SODIUM ION (NAa)
7b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
4
GAR
2
Ligand/Ion
GLYCINAMIDE RIBONUCLEOTIDE
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
MPO
1
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
7
NA
-1
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 , HOH A:410 , HOH A:533
BINDING SITE FOR RESIDUE MG A 393
02
AC2
SOFTWARE
ATP A:1 , GLU A:267 , GLU A:279 , HOH A:404
BINDING SITE FOR RESIDUE MG A 394
03
AC3
SOFTWARE
GLU B:279 , ATP B:397 , HOH B:684
BINDING SITE FOR RESIDUE MG B 393
04
AC4
SOFTWARE
GLU B:267 , GLU B:279 , ATP B:397 , HOH B:605
BINDING SITE FOR RESIDUE MG B 394
05
AC5
SOFTWARE
ASN A:100 , VAL A:101 , PRO A:103 , HOH A:797
BINDING SITE FOR RESIDUE NA A 395
06
AC6
SOFTWARE
ASN B:100 , VAL B:101 , PRO B:103 , HOH B:493 , HOH B:540
BINDING SITE FOR RESIDUE NA B 395
07
AC7
SOFTWARE
GLU A:84
BINDING SITE FOR RESIDUE CL A 396
08
AC8
SOFTWARE
GLN A:341 , VAL A:374 , HOH A:725 , HOH A:732
BINDING SITE FOR RESIDUE CL A 397
09
AC9
SOFTWARE
HIS B:216 , PHE B:217 , HOH B:500
BINDING SITE FOR RESIDUE CL B 396
10
BC1
SOFTWARE
ARG A:33 , HOH A:509 , ARG B:33 , EDO B:399
BINDING SITE FOR RESIDUE CL A 398
11
BC2
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 , GAR A:399 , HOH A:402 , HOH A:404 , HOH A:410 , HOH A:455 , HOH A:462 , HOH A:479 , HOH A:527 , HOH A:533 , HOH A:619 , HOH A:770 , HOH A:901
BINDING SITE FOR RESIDUE ATP A 1
12
BC3
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 , VAL B:198 , GLU B:203 , GLU B:267 , PHE B:269 , GLU B:279 , MG B:393 , MG B:394 , HOH B:489 , HOH B:511 , HOH B:605
BINDING SITE FOR RESIDUE ATP B 397
13
BC4
SOFTWARE
ATP A:1 , GLY A:21 , GLU A:22 , LEU A:23 , GLU A:82 , ILE A:83 , SER A:160 , SER A:161 , ASP A:286 , LYS A:355 , ARG A:362 , ARG A:363 , HOH A:405 , HOH A:413 , HOH A:421 , HOH A:433 , HOH A:441 , HOH A:446 , HOH A:513 , HOH A:517 , HOH A:551 , HOH A:574
BINDING SITE FOR RESIDUE GAR A 399
14
BC5
SOFTWARE
GLY B:21 , GLU B:22 , LEU B:23 , GLU B:82 , ILE B:83 , ASP B:286 , LYS B:355 , ARG B:362 , ARG B:363 , HOH B:404 , HOH B:411 , HOH B:423 , HOH B:435 , HOH B:495 , HOH B:607 , HOH B:651
BINDING SITE FOR RESIDUE GAR B 398
15
BC6
SOFTWARE
ASP A:46 , MET A:50 , HIS A:51 , ARG A:55 , SER A:56 , GLU A:143 , HOH A:460 , HOH A:476 , HOH A:552 , HOH A:832 , HOH A:871 , LEU B:8 , HIS B:54
BINDING SITE FOR RESIDUE MPO A 400
16
BC7
SOFTWARE
CL A:398 , GLU B:30 , ARG B:33 , ASP B:296 , LEU B:297 , SER B:298 , ALA B:301 , HOH B:440 , HOH B:453 , HOH B:614
BINDING SITE FOR RESIDUE EDO B 399
17
BC8
SOFTWARE
SER B:240 , PRO B:241 , LEU B:242 , HOH B:642
BINDING SITE FOR RESIDUE EDO B 400
18
BC9
SOFTWARE
ARG A:106 , LYS A:109
BINDING SITE FOR RESIDUE EDO A 401
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1kj8a1 (A:319-392)
1b: SCOP_d1kj8b1 (B:319-392)
2a: SCOP_d1kj8a3 (A:113-318)
2b: SCOP_d1kj8b3 (B:113-318)
3a: SCOP_d1kj8a2 (A:2-112)
3b: SCOP_d1kj8b2 (B:2-112)
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(
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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
d1kj8a1
A:319-392
1b
d1kj8b1
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
d1kj8a3
A:113-318
2b
d1kj8b3
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
d1kj8a2
A:2-112
3b
d1kj8b2
B:2-112
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1kj8A03 (A:197-391)
1b: CATH_1kj8B03 (B:197-391)
2a: CATH_1kj8A02 (A:123-196)
2b: CATH_1kj8B02 (B:123-196)
3a: CATH_1kj8A01 (A:2-122)
3b: CATH_1kj8B01 (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
1kj8A03
A:197-391
1b
1kj8B03
B:197-391
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Escherichia coli. Organism_taxid: 562.
(15)
2a
1kj8A02
A:123-196
2b
1kj8B02
B: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
1kj8A01
A:2-122
3b
1kj8B01
B:2-122
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Pfam Domains
(0, 0)
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