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1KJJ
Biol. Unit 1
Info
Asym.Unit (141 KB)
Biol.Unit 1 (135 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCNIAMIDE RIBONUCLEOTIDE TRANSFORMYLASE IN COMPLEX WITH MG-ATP-GAMMA-S
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
:
1.75
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
(2, 3)
Info
All Hetero Components
1a: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSa)
1b: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSb)
2a: CHLORIDE ION (CLa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
5a: SODIUM ION (NAa)
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Label:
No.
Name
Count
Type
Full Name
1
AGS
2
Ligand/Ion
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
MPO
1
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
5
NA
-1
Ligand/Ion
SODIUM ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
AGS A:1 , GLU A:279 , HOH A:627 , HOH A:736
BINDING SITE FOR RESIDUE MG A 393
2
AC2
SOFTWARE
AGS A:1 , GLU A:267 , GLU A:279 , HOH A:467
BINDING SITE FOR RESIDUE MG A 394
3
AC3
SOFTWARE
GLU B:279 , AGS B:395 , HOH B:479 , HOH B:626
BINDING SITE FOR RESIDUE MG B 393
4
AC4
SOFTWARE
GLU B:267 , GLU B:279 , AGS B:395 , HOH B:527
BINDING SITE FOR RESIDUE MG B 394
5
AC5
SOFTWARE
ASN A:100 , VAL A:101 , PRO A:103 , HOH A:432
BINDING SITE FOR RESIDUE NA A 395
6
AC6
SOFTWARE
ARG A:43 , VAL A:58 , ARG A:119 , PHE A:134 , HOH A:741
BINDING SITE FOR RESIDUE CL A 396
7
AC7
SOFTWARE
ARG A:114 , SER A:130 , 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 , GLU A:203 , GLN A:225 , GLU A:267 , PHE A:269 , GLU A:279 , MG A:393 , MG A:394 , HOH A:467 , HOH A:471 , HOH A:495 , HOH A:497 , HOH A:514 , HOH A:617 , HOH A:702 , HOH A:736
BINDING SITE FOR RESIDUE AGS A 1
8
AC8
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:197 , VAL B:198 , GLU B:203 , GLU B:267 , GLU B:279 , MG B:393 , MG B:394 , HOH B:461 , HOH B:527 , HOH B:626
BINDING SITE FOR RESIDUE AGS B 395
9
AC9
SOFTWARE
ASP A:46 , MET A:50 , HIS A:51 , ARG A:55 , SER A:56 , GLU A:143 , HOH A:402 , HOH A:465 , HOH A:523 , LEU B:8 , HIS B:54
BINDING SITE FOR RESIDUE MPO A 397
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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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_d1kjja1 (A:319-392)
1b: SCOP_d1kjjb1 (B:319-392)
2a: SCOP_d1kjja3 (A:113-318)
2b: SCOP_d1kjjb3 (B:113-318)
3a: SCOP_d1kjja2 (A:2-112)
3b: SCOP_d1kjjb2 (B:2-112)
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Families
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)
(
)
Protein Domains
(
)
(
)
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
d1kjja1
A:319-392
1b
d1kjjb1
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
d1kjja3
A:113-318
2b
d1kjjb3
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
d1kjja2
A:2-112
3b
d1kjjb2
B:2-112
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1kjjA03 (A:197-391)
1b: CATH_1kjjB03 (B:197-391)
2a: CATH_1kjjA02 (A:123-196)
2b: CATH_1kjjB02 (B:123-196)
3a: CATH_1kjjA01 (A:2-122)
3b: CATH_1kjjB01 (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
1kjjA03
A:197-391
1b
1kjjB03
B:197-391
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Escherichia coli. Organism_taxid: 562.
(15)
2a
1kjjA02
A:123-196
2b
1kjjB02
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
1kjjA01
A:2-122
3b
1kjjB01
B:2-122
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (141 KB)
Header - Asym.Unit
Biol.Unit 1 (135 KB)
Header - Biol.Unit 1
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