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1KJQ
Biol. Unit 1
Info
Asym.Unit (153 KB)
Biol.Unit 1 (147 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE IN COMPLEX WITH MG-ADP
Authors
:
J. B. Thoden, S. M. Firestine, S. J. Benkovic, H. M. Holden
Date
:
05 Dec 01 (Deposition) - 28 Jun 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.05
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
(3, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
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)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
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
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
MPO
1
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
6
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(26, 26)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ADP A:1 , GLU A:267 , GLU A:279 , HOH A:485 , HOH A:841
BINDING SITE FOR RESIDUE MG A 393
02
AC2
SOFTWARE
GLU B:267 , GLU B:279 , ADP B:397 , HOH B:470 , HOH B:767
BINDING SITE FOR RESIDUE MG B 393
03
AC3
SOFTWARE
ALA A:53 , HOH A:505 , HOH A:586 , HOH A:811 , HOH A:920 , MET B:50 , HIS B:51 , HOH B:555
BINDING SITE FOR RESIDUE NA B 394
04
AC4
SOFTWARE
ASN A:100 , VAL A:101 , PRO A:103 , HOH A:432 , HOH A:445 , HOH A:821
BINDING SITE FOR RESIDUE NA A 394
05
AC5
SOFTWARE
ARG A:43 , VAL A:58 , ARG A:119 , ARG A:133 , PHE A:134 , HOH A:699 , HOH A:809
BINDING SITE FOR RESIDUE CL A 395
06
AC6
SOFTWARE
ARG A:43 , THR A:131 , TYR A:132 , HOH A:468
BINDING SITE FOR RESIDUE CL A 396
07
AC7
SOFTWARE
HIS B:216 , PHE B:217 , HOH B:488 , HOH B:644
BINDING SITE FOR RESIDUE CL B 395
08
AC8
SOFTWARE
HOH A:415 , PHE B:337 , GLY B:354
BINDING SITE FOR RESIDUE CL B 396
09
AC9
SOFTWARE
ARG A:114 , SER A:130 , ILE A:153 , LYS A:155 , GLN A:165 , GLU A:195 , GLY A:196 , VAL A:197 , VAL A:198 , PHE A:200 , GLU A:203 , GLN A:225 , GLU A:267 , PHE A:269 , GLU A:279 , MG A:393 , HOH A:465 , HOH A:479 , HOH A:485 , HOH A:552 , HOH A:556 , HOH A:595 , HOH A:760 , HOH A:841
BINDING SITE FOR RESIDUE ADP A 1
10
BC1
SOFTWARE
ARG B:114 , SER B:130 , ILE B:153 , LYS B:155 , GLN B:165 , GLU B:195 , GLY B:196 , VAL B:198 , GLU B:203 , GLN B:225 , GLU B:267 , PHE B:269 , GLU B:279 , MG B:393 , HOH B:470 , HOH B:492 , HOH B:505 , HOH B:582 , HOH B:604 , HOH B:756 , HOH B:761 , HOH B:767 , HOH B:775 , HOH B:776
BINDING SITE FOR RESIDUE ADP B 397
11
BC2
SOFTWARE
ASP A:46 , MET A:50 , HIS A:51 , ARG A:55 , SER A:56 , GLU A:143 , HOH A:460 , HOH A:500 , HOH A:509 , HOH A:688 , LEU B:8 , HIS B:54
BINDING SITE FOR RESIDUE MPO A 397
12
BC3
SOFTWARE
LEU A:34 , ARG A:305 , HOH A:438 , HOH A:629 , GLN B:349 , ILE B:350
BINDING SITE FOR RESIDUE EDO A 398
13
BC4
SOFTWARE
EDO A:406 , HOH A:506 , HOH A:514 , GLU B:30 , ARG B:33 , ASP B:296 , LEU B:297 , SER B:298 , ALA B:301 , HOH B:406 , HOH B:482
BINDING SITE FOR RESIDUE EDO B 398
14
BC5
SOFTWARE
ILE A:378 , HOH A:934 , HOH B:627
BINDING SITE FOR RESIDUE EDO A 399
15
BC6
SOFTWARE
GLY B:21 , GLU B:22 , LEU B:23 , GLY B:24 , GLU B:82 , HOH B:576 , HOH B:709 , HOH B:714 , HOH B:807
BINDING SITE FOR RESIDUE EDO B 399
16
BC7
SOFTWARE
ARG A:246 , GLU A:274 , VAL A:275 , HOH A:585 , HOH A:680
BINDING SITE FOR RESIDUE EDO A 400
17
BC8
SOFTWARE
ARG A:69 , HOH A:542 , HOH A:578 , HOH A:877
BINDING SITE FOR RESIDUE EDO A 401
18
BC9
SOFTWARE
THR A:2 , LEU A:3 , TYR A:78 , HOH A:549 , HOH A:700 , HOH A:765
BINDING SITE FOR RESIDUE EDO A 402
19
CC1
SOFTWARE
PRO B:328 , GLN B:329 , LEU B:330 , VAL B:390 , HOH B:409 , HOH B:483
BINDING SITE FOR RESIDUE EDO B 400
20
CC2
SOFTWARE
ASN A:60 , ASP A:63 , ALA A:122 , THR A:129 , TYR A:132 , HOH A:568 , HOH A:571 , HOH A:898
BINDING SITE FOR RESIDUE EDO A 403
21
CC3
SOFTWARE
GLU A:379 , HIS A:383 , HOH A:456 , HOH A:675 , HOH A:803 , HOH A:947 , HOH A:948
BINDING SITE FOR RESIDUE EDO A 404
22
CC4
SOFTWARE
ARG A:231 , HOH A:497 , HOH A:589 , HOH A:915 , HOH A:927
BINDING SITE FOR RESIDUE EDO A 405
23
CC5
SOFTWARE
PHE B:134 , ALA B:135 , LEU B:140 , ALA B:144 , HOH B:655 , HOH B:787
BINDING SITE FOR RESIDUE EDO B 401
24
CC6
SOFTWARE
LEU B:244 , GLU B:245 , GLN B:248 , HOH B:559 , HOH B:583
BINDING SITE FOR RESIDUE EDO B 402
25
CC7
SOFTWARE
LEU A:292 , ILE A:293 , GLN A:349 , ARG A:351 , HOH A:452 , HOH A:478 , HOH A:514 , HOH A:843 , ASP B:296 , EDO B:398
BINDING SITE FOR RESIDUE EDO A 406
26
CC8
SOFTWARE
GLY A:64 , ALA A:87 , MET A:90 , GLN A:93
BINDING SITE FOR RESIDUE EDO A 407
[
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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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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1kjqa1 (A:319-392)
1b: SCOP_d1kjqb1 (B:319-392)
2a: SCOP_d1kjqa3 (A:113-318)
2b: SCOP_d1kjqb3 (B:113-318)
3a: SCOP_d1kjqa2 (A:2-112)
3b: SCOP_d1kjqb2 (B:2-112)
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Classes
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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
d1kjqa1
A:319-392
1b
d1kjqb1
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
d1kjqa3
A:113-318
2b
d1kjqb3
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
d1kjqa2
A:2-112
3b
d1kjqb2
B:2-112
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1kjqB03 (B:197-390)
1b: CATH_1kjqA03 (A:197-391)
2a: CATH_1kjqA02 (A:123-196)
2b: CATH_1kjqB02 (B:123-196)
3a: CATH_1kjqA01 (A:2-122)
3b: CATH_1kjqB01 (B:2-122)
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Topologies
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)
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)
Homologous Superfamilies
(
)
(
)
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
1kjqB03
B:197-390
1b
1kjqA03
A:197-391
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Escherichia coli. Organism_taxid: 562.
(15)
2a
1kjqA02
A:123-196
2b
1kjqB02
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
1kjqA01
A:2-122
3b
1kjqB01
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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Asym.Unit (153 KB)
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