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3KAL
Asym. Unit
Info
Asym.Unit (184 KB)
Biol.Unit 1 (176 KB)
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(1)
Title
:
STRUCTURE OF HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN CLOSED CONFORMATION WITH HOMOGLUTATHIONE, ADP, A SULFATE ION, AND THREE MAGNESIUM IONS BOUND
Authors
:
A. Galant, K. A. J. Arkus, C. Zubieta, R. E. Cahoon, J. M. Jez
Date
:
19 Oct 09 (Deposition) - 22 Dec 09 (Release) - 12 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dimer, Atp-Grasp Domain, Homoglutathione
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Galant, K. A. Arkus, C. Zubieta, R. E. Cahoon, J. M. Jez
Structural Basis For Evolution Of Product Diversity In Soybean Glutathione Biosynthesis.
Plant Cell V. 21 3450 2009
(for further references see the
PDB file header
)
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Hetero Components
(4, 14)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: D-GAMMA-GLUTAMYL-L-CYSTEINYL-BETA-... (HGSa)
2b: D-GAMMA-GLUTAMYL-L-CYSTEINYL-BETA-... (HGSb)
2c: D-GAMMA-GLUTAMYL-L-CYSTEINYL-BETA-... (HGSc)
2d: D-GAMMA-GLUTAMYL-L-CYSTEINYL-BETA-... (HGSd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
HGS
4
Ligand/Ion
D-GAMMA-GLUTAMYL-L-CYSTEINYL-BETA-ALANINE
3
MG
6
Ligand/Ion
MAGNESIUM ION
4
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(14, 14)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:168 , GLU A:169 , LYS A:334 , VAL A:386 , LYS A:388 , GLU A:392 , GLY A:393 , GLY A:394 , ASN A:397 , TYR A:399 , MET A:424 , GLN A:425 , ARG A:426 , ILE A:427 , GLU A:450 , LYS A:477 , MG A:502 , MG A:503 , SO4 A:505 , HOH A:588 , HOH A:650 , HOH A:683 , HOH A:710 , HOH A:734 , HOH A:864
BINDING SITE FOR RESIDUE ADP A 500
02
AC2
SOFTWARE
ARG A:153 , ASN A:171 , ILE A:173 , SER A:174 , THR A:175 , SER A:176 , PHE A:177 , GLN A:238 , GLU A:241 , ASN A:243 , ARG A:295 , TYR A:298 , ARG A:475 , VAL A:486 , LEU A:487 , SO4 A:505 , HOH A:688 , HOH A:835
BINDING SITE FOR RESIDUE HGS A 501
03
AC3
SOFTWARE
GLU A:169 , ASN A:171 , GLU A:392 , ADP A:500 , SO4 A:505
BINDING SITE FOR RESIDUE MG A 502
04
AC4
SOFTWARE
GLU A:169 , ADP A:500 , SO4 A:505 , HOH A:588 , HOH A:710
BINDING SITE FOR RESIDUE MG A 503
05
AC5
SOFTWARE
GLU A:169 , MET A:170 , GLY A:332 , GLU A:392 , HOH A:566 , HOH A:634
BINDING SITE FOR RESIDUE MG A 504
06
AC6
SOFTWARE
ARG A:153 , ASP A:155 , GLU A:169 , ASN A:171 , GLU A:392 , GLY A:393 , ARG A:475 , ADP A:500 , HGS A:501 , MG A:502 , MG A:503 , HOH A:588 , HOH A:710
BINDING SITE FOR RESIDUE SO4 A 505
07
AC7
SOFTWARE
TRP A:49 , ASN A:53 , CYS A:182 , LEU A:183 , GLY A:186 , ASN A:209 , ASN A:210 , VAL A:212 , ASP A:213 , HOH A:658 , HOH A:675 , HOH A:747 , HOH A:828 , HOH A:854 , HOH A:861
BINDING SITE FOR RESIDUE HGS A 506
08
AC8
SOFTWARE
ILE B:168 , GLU B:169 , LYS B:334 , VAL B:386 , LYS B:388 , ARG B:391 , GLU B:392 , GLY B:393 , GLY B:394 , ASN B:396 , ASN B:397 , TYR B:399 , MET B:424 , GLN B:425 , ARG B:426 , ILE B:427 , GLU B:450 , LYS B:477 , MG B:502 , MG B:503 , SO4 B:505 , HOH B:627 , HOH B:663 , HOH B:684 , HOH B:758 , HOH B:800
BINDING SITE FOR RESIDUE ADP B 500
09
AC9
SOFTWARE
ARG B:153 , ASN B:171 , ILE B:173 , SER B:174 , THR B:175 , SER B:176 , GLN B:238 , GLU B:241 , ASN B:243 , ARG B:295 , TYR B:298 , ARG B:475 , GLY B:485 , VAL B:486 , SO4 B:505 , HOH B:545 , HOH B:551 , HOH B:688 , HOH B:807
BINDING SITE FOR RESIDUE HGS B 501
10
BC1
SOFTWARE
GLU B:169 , ASN B:171 , GLU B:392 , ADP B:500 , SO4 B:505
BINDING SITE FOR RESIDUE MG B 502
11
BC2
SOFTWARE
GLU B:169 , ADP B:500 , SO4 B:505 , HOH B:627 , HOH B:663
BINDING SITE FOR RESIDUE MG B 503
12
BC3
SOFTWARE
GLU B:169 , MET B:170 , GLY B:332 , GLU B:392 , HOH B:537
BINDING SITE FOR RESIDUE MG B 504
13
BC4
SOFTWARE
ARG B:153 , ASP B:155 , GLU B:169 , ASN B:171 , GLU B:392 , GLY B:393 , ARG B:475 , ADP B:500 , HGS B:501 , MG B:502 , MG B:503 , HOH B:627 , HOH B:663
BINDING SITE FOR RESIDUE SO4 B 505
14
BC5
SOFTWARE
ASN B:53 , CYS B:182 , LEU B:183 , ASP B:213 , HOH B:536 , HOH B:655 , HOH B:828 , HOH B:834
BINDING SITE FOR RESIDUE HGS B 506
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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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
(0, 0)
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CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_3kalA02 (A:84-95,A:143-182,A:443-498)
1b: CATH_3kalB02 (B:84-95,B:143-182,B:443-498)
2a: CATH_3kalA05 (A:366-431)
2b: CATH_3kalB05 (B:366-431)
3a: CATH_3kalA04 (A:209-332)
3b: CATH_3kalB04 (B:209-332)
4a: CATH_3kalA03 (A:96-142,A:333-365)
4b: CATH_3kalB03 (B:96-142,B:333-365)
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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)
Glycine max. Organism_taxid: 3847.
(1)
1a
3kalA02
A:84-95,A:143-182,A:443-498
1b
3kalB02
B:84-95,B:143-182,B:443-498
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.50, no name defined]
(4)
Glycine max. Organism_taxid: 3847.
(1)
2a
3kalA05
A:366-431
2b
3kalB05
B:366-431
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1760, no name defined]
(6)
Glycine max. Organism_taxid: 3847.
(1)
3a
3kalA04
A:209-332
3b
3kalB04
B:209-332
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Glutathione Synthetase; Chain A, domain 3
(6)
Homologous Superfamily
:
Glutathione Synthetase; Chain A, domain 3
(6)
Glycine max. Organism_taxid: 3847.
(1)
4a
3kalA03
A:96-142,A:333-365
4b
3kalB03
B:96-142,B:333-365
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_GSH_synthase_3kalB01 (B:229-331)
1b: PFAM_GSH_synthase_3kalB02 (B:229-331)
2a: PFAM_GSH_synth_ATP_3kalB03 (B:29-498)
2b: PFAM_GSH_synth_ATP_3kalB04 (B:29-498)
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Organisms
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)
(
)
Clan
:
PreATP-grasp
(8)
Family
:
GSH_synthase
(4)
Glycine max (Soybean) (Glycine hispida)
(3)
1a
GSH_synthase-3kalB01
B:229-331
1b
GSH_synthase-3kalB02
B:229-331
Clan
:
no clan defined [family: GSH_synth_ATP]
(4)
Family
:
GSH_synth_ATP
(4)
Glycine max (Soybean) (Glycine hispida)
(3)
2a
GSH_synth_ATP-3kalB03
B:29-498
2b
GSH_synth_ATP-3kalB04
B:29-498
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