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1KJI
Asym. Unit
Info
Asym.Unit (148 KB)
Biol.Unit 1 (141 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE IN COMPLEX WITH MG-AMPPCP
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, 12)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPa)
1b: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPb)
2a: CHLORIDE ION (CLa)
3a: 1,2-ETHANEDIOL (EDOa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
5a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
6c: SODIUM ION (NAc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ACP
2
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2
CL
1
Ligand/Ion
CHLORIDE ION
3
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
4
MG
4
Ligand/Ion
MAGNESIUM ION
5
MPO
1
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
6
NA
3
Ligand/Ion
SODIUM ION
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ACP A:1 , GLU A:279 , HOH A:509 , HOH A:536
BINDING SITE FOR RESIDUE MG A 393
02
AC2
SOFTWARE
ACP A:1 , GLU A:267 , GLU A:279 , HOH A:465
BINDING SITE FOR RESIDUE MG A 394
03
AC3
SOFTWARE
GLU B:279 , ACP B:396 , HOH B:470 , HOH B:547
BINDING SITE FOR RESIDUE MG B 393
04
AC4
SOFTWARE
GLU B:267 , GLU B:279 , ACP B:396 , HOH B:635
BINDING SITE FOR RESIDUE MG B 394
05
AC5
SOFTWARE
ALA A:53 , HOH A:453 , HOH A:521 , ALA B:53 , HOH B:456 , HOH B:651 , HOH B:745
BINDING SITE FOR RESIDUE NA A 395
06
AC6
SOFTWARE
GLU A:95 , ASN A:100 , VAL A:101 , HOH A:567 , HOH A:637
BINDING SITE FOR RESIDUE NA A 396
07
AC7
SOFTWARE
ASN B:100 , VAL B:101 , PRO B:103 , HOH B:461 , HOH B:690
BINDING SITE FOR RESIDUE NA B 395
08
AC8
SOFTWARE
ARG A:43 , VAL A:58 , ARG A:119 , ARG A:133 , PHE A:134 , HOH A:590
BINDING SITE FOR RESIDUE CL A 397
09
AC9
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 , GLU A:203 , GLN A:225 , GLU A:267 , PHE A:269 , GLU A:279 , MG A:393 , MG A:394 , HOH A:432 , HOH A:465 , HOH A:475 , HOH A:485 , HOH A:509 , HOH A:562 , HOH A:563 , HOH A:644 , HOH A:758
BINDING SITE FOR RESIDUE ACP A 1
10
BC1
SOFTWARE
ARG B:114 , SER B:130 , LYS B:155 , SER B:159 , SER B:160 , SER B:161 , GLY B:162 , GLU B:195 , GLY B:196 , VAL B:198 , GLU B:203 , GLU B:267 , GLU B:279 , MG B:393 , MG B:394 , HOH B:547 , HOH B:553 , HOH B:572 , HOH B:635 , HOH B:767
BINDING SITE FOR RESIDUE ACP B 396
11
BC2
SOFTWARE
ASP A:46 , MET A:50 , HIS A:51 , ARG A:55 , SER A:56 , GLU A:143 , HOH A:437 , HOH A:453 , HOH A:468 , HOH A:685 , HOH A:727 , LEU B:8 , HIS B:54
BINDING SITE FOR RESIDUE MPO A 398
12
BC3
SOFTWARE
ASP A:63 , THR A:129 , SER A:130 , THR A:131 , TYR A:132 , HOH A:502
BINDING SITE FOR RESIDUE EDO A 399
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1kjia1 (A:319-392)
1b: SCOP_d1kjib1 (B:319-392)
2a: SCOP_d1kjia3 (A:113-318)
2b: SCOP_d1kjib3 (B:113-318)
3a: SCOP_d1kjia2 (A:2-112)
3b: SCOP_d1kjib2 (B:2-112)
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Classes
(
)
(
)
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(
)
(
)
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(
)
(
)
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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
d1kjia1
A:319-392
1b
d1kjib1
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
d1kjia3
A:113-318
2b
d1kjib3
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
d1kjia2
A:2-112
3b
d1kjib2
B:2-112
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1kjiA03 (A:197-391)
1b: CATH_1kjiB03 (B:197-391)
2a: CATH_1kjiA02 (A:123-196)
2b: CATH_1kjiB02 (B:123-196)
3a: CATH_1kjiA01 (A:2-122)
3b: CATH_1kjiB01 (B:2-122)
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)
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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
1kjiA03
A:197-391
1b
1kjiB03
B:197-391
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Escherichia coli. Organism_taxid: 562.
(15)
2a
1kjiA02
A:123-196
2b
1kjiB02
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
1kjiA01
A:2-122
3b
1kjiB01
B:2-122
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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