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1KH3
Asym. Unit
Info
Asym.Unit (269 KB)
Biol.Unit 1 (262 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS HB8 ARGININOSUCCINATE SYNTHETASE IN COMPLEX WITH INHIBITOR
Authors
:
M. Goto, K. Hirotsu, I. Miyahara, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
29 Nov 01 (Deposition) - 22 Apr 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Ligase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Goto, R. Omi, I. Miyahara, M. Sugahara, K. Hirotsu
Structures Of Argininosuccinate Synthetase In Enzyme-Atp Substrates And Enzyme-Amp Product Forms: Stereochemistry Of The Catalytic Reaction
J. Biol. Chem. V. 278 22964 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 20)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
1d: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPd)
2a: ARGININE (ARGa)
2b: ARGININE (ARGb)
2c: ARGININE (ARGc)
2d: ARGININE (ARGd)
3a: ASPARTIC ACID (ASPa)
3b: ASPARTIC ACID (ASPb)
3c: ASPARTIC ACID (ASPc)
3d: ASPARTIC ACID (ASPd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
4
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
ARG
4
Mod. Amino Acid
ARGININE
3
ASP
4
Mod. Amino Acid
ASPARTIC ACID
4
MG
4
Ligand/Ion
MAGNESIUM ION
5
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:8 , GLY A:10 , LEU A:11 , ASP A:12 , THR A:13 , ANP A:510
BINDING SITE FOR RESIDUE SO4 A 540
02
AC2
SOFTWARE
SER B:8 , GLY B:10 , ASP B:12 , THR B:13 , HOH B:1373 , ANP B:4510
BINDING SITE FOR RESIDUE SO4 B 4540
03
AC3
SOFTWARE
SER C:8 , GLY C:10 , LEU C:11 , ASP C:12 , THR C:13 , ANP C:2510
BINDING SITE FOR RESIDUE SO4 C 2540
04
AC4
SOFTWARE
SER D:8 , GLY D:10 , LEU D:11 , ASP D:12 , THR D:13 , ANP D:3510
BINDING SITE FOR RESIDUE SO4 D 3540
05
AC5
SOFTWARE
ANP A:510 , HOH A:1001 , HOH A:1005 , HOH A:1006
BINDING SITE FOR RESIDUE MG A 550
06
AC6
SOFTWARE
HOH A:1008 , HOH B:1002 , HOH B:1007 , ANP B:4510
BINDING SITE FOR RESIDUE MG B 4550
07
AC7
SOFTWARE
HOH C:1003 , HOH C:1009 , HOH C:1010 , ANP C:2510
BINDING SITE FOR RESIDUE MG C 2550
08
AC8
SOFTWARE
HOH D:1004 , HOH D:1011 , HOH D:1012 , ANP D:3510
BINDING SITE FOR RESIDUE MG D 3550
09
AC9
SOFTWARE
ALA A:6 , THR A:13 , PHE A:31 , THR A:32 , ALA A:33 , GLN A:37 , ARG A:92 , HIS A:113 , GLY A:114 , PHE A:125 , SER A:173 , MET A:174 , ARG A:520 , ASP A:530 , SO4 A:540 , MG A:550 , HOH A:1005 , HOH A:1494 , HOH A:1536
BINDING SITE FOR RESIDUE ANP A 510
10
BC1
SOFTWARE
HOH A:1008 , ARG A:4520 , ASP A:4530 , ALA B:6 , TYR B:7 , THR B:13 , PHE B:31 , THR B:32 , ALA B:33 , GLN B:37 , ARG B:92 , HIS B:113 , GLY B:114 , PHE B:125 , SER B:173 , MET B:174 , HOH B:1237 , HOH B:1396 , HOH B:1501 , SO4 B:4540 , MG B:4550
BINDING SITE FOR RESIDUE ANP B 4510
11
BC2
SOFTWARE
ARG A:2520 , ASP A:2530 , ALA C:6 , THR C:13 , PHE C:31 , THR C:32 , ALA C:33 , GLN C:37 , ARG C:92 , HIS C:113 , GLY C:114 , PHE C:125 , SER C:173 , MET C:174 , HOH C:1010 , HOH C:1440 , SO4 C:2540 , MG C:2550
BINDING SITE FOR RESIDUE ANP C 2510
12
BC3
SOFTWARE
ARG A:3520 , ASP A:3530 , ALA D:6 , TYR D:7 , THR D:13 , PHE D:31 , ALA D:33 , GLN D:37 , ARG D:92 , HIS D:113 , GLY D:114 , PHE D:125 , SER D:173 , MET D:174 , HOH D:1004 , SO4 D:3540 , MG D:3550
BINDING SITE FOR RESIDUE ANP D 3510
13
BC4
SOFTWARE
TYR A:84 , THR A:88 , SER A:89 , ASN A:120 , ARG A:124 , SER A:173 , MET A:174 , ASP A:175 , SER A:182 , TYR A:183 , GLU A:184 , GLU A:258 , TYR A:270 , TYR A:310 , ANP A:510 , HOH A:1013
BINDING SITE FOR RESIDUE ARG A 520
14
BC5
SOFTWARE
HOH A:1038 , TYR B:84 , THR B:88 , SER B:89 , ASN B:120 , ARG B:124 , SER B:173 , MET B:174 , ASP B:175 , SER B:182 , GLU B:184 , GLU B:258 , TYR B:270 , TYR B:310 , ANP B:4510
BINDING SITE FOR RESIDUE ARG A 4520
15
BC6
SOFTWARE
HOH A:1042 , TYR C:84 , THR C:88 , SER C:89 , ASN C:120 , ARG C:124 , SER C:173 , MET C:174 , ASP C:175 , SER C:182 , GLU C:184 , GLU C:258 , TYR C:270 , TYR C:310 , ANP C:2510
BINDING SITE FOR RESIDUE ARG A 2520
16
BC7
SOFTWARE
HOH A:1156 , TYR D:84 , THR D:88 , SER D:89 , ASN D:120 , ARG D:124 , SER D:173 , MET D:174 , ASP D:175 , SER D:182 , GLU D:184 , GLU D:258 , TYR D:270 , TYR D:310 , ANP D:3510
BINDING SITE FOR RESIDUE ARG A 3520
17
BC8
SOFTWARE
ALA A:115 , THR A:116 , GLY A:119 , ASN A:120 , ASP A:121 , ANP A:510 , HOH A:1005 , HOH A:1013 , HOH A:1039 , HOH A:1244
BINDING SITE FOR RESIDUE ASP A 530
18
BC9
SOFTWARE
HOH A:1008 , HOH A:1038 , HOH A:1409 , ALA B:115 , THR B:116 , GLY B:119 , ASN B:120 , ASP B:121 , HOH B:1090 , ANP B:4510
BINDING SITE FOR RESIDUE ASP A 4530
19
CC1
SOFTWARE
HOH A:1042 , HOH A:1291 , ALA C:115 , THR C:116 , GLY C:119 , ASN C:120 , ASP C:121 , HOH C:1010 , HOH C:1067 , ANP C:2510
BINDING SITE FOR RESIDUE ASP A 2530
20
CC2
SOFTWARE
HOH A:1156 , HOH A:1229 , ALA D:115 , THR D:116 , GLY D:119 , ASN D:120 , ASP D:121 , GLU D:184 , HOH D:1004 , HOH D:1137 , ANP D:3510
BINDING SITE FOR RESIDUE ASP A 3530
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ARGININOSUCCIN_SYN_1 (A:6-14,B:6-14,C:6-14,D:6-14)
2: ARGININOSUCCIN_SYN_2 (A:114-125,B:114-125,C:114-125,D:11...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ARGININOSUCCIN_SYN_1
PS00564
Argininosuccinate synthase signature 1.
ASSY_THET8
6-14
4
A:6-14
B:6-14
C:6-14
D:6-14
2
ARGININOSUCCIN_SYN_2
PS00565
Argininosuccinate synthase signature 2.
ASSY_THET8
114-125
4
A:114-125
B:114-125
C:114-125
D:114-125
[
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Exons
(0, 0)
Info
All Exons
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1kh3a2 (A:171-395)
1b: SCOP_d1kh3b2 (B:171-395)
1c: SCOP_d1kh3c2 (C:171-395)
1d: SCOP_d1kh3d2 (D:171-395)
2a: SCOP_d1kh3a1 (A:1-165)
2b: SCOP_d1kh3b1 (B:1-165)
2c: SCOP_d1kh3c1 (C:1-165)
2d: SCOP_d1kh3d1 (D:1-165)
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Superfamilies
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)
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)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Argininosuccinate synthetase, C-terminal domain
(14)
Superfamily
:
Argininosuccinate synthetase, C-terminal domain
(14)
Family
:
Argininosuccinate synthetase, C-terminal domain
(12)
Protein domain
:
Argininosuccinate synthetase, C-terminal domain
(12)
Thermus thermophilus [TaxId: 274]
(7)
1a
d1kh3a2
A:171-395
1b
d1kh3b2
B:171-395
1c
d1kh3c2
C:171-395
1d
d1kh3d2
D:171-395
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Adenine nucleotide alpha hydrolases-like
(110)
Family
:
N-type ATP pyrophosphatases
(44)
Protein domain
:
Argininosuccinate synthetase, N-terminal domain
(12)
Thermus thermophilus [TaxId: 274]
(7)
2a
d1kh3a1
A:1-165
2b
d1kh3b1
B:1-165
2c
d1kh3c1
C:1-165
2d
d1kh3d1
D:1-165
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1kh3A01 (A:1-171)
1b: CATH_1kh3B01 (B:1-171)
1c: CATH_1kh3C01 (C:1-171)
1d: CATH_1kh3D01 (D:1-171)
2a: CATH_1kh3A02 (A:172-395)
2b: CATH_1kh3B02 (B:172-395)
2c: CATH_1kh3C02 (C:172-395)
2d: CATH_1kh3D02 (D:172-395)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Thermus thermophilus. Organism_taxid: 274.
(11)
1a
1kh3A01
A:1-171
1b
1kh3B01
B:1-171
1c
1kh3C01
C:1-171
1d
1kh3D01
D:1-171
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Argininosuccinate synthetase, chain A, domain 2
(13)
Homologous Superfamily
:
Argininosuccinate synthetase, chain A, domain 2
(13)
Thermus thermophilus. Organism_taxid: 274.
(7)
2a
1kh3A02
A:172-395
2b
1kh3B02
B:172-395
2c
1kh3C02
C:172-395
2d
1kh3D02
D:172-395
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Arginosuc_synth_1kh3D01 (D:4-391)
1b: PFAM_Arginosuc_synth_1kh3D02 (D:4-391)
1c: PFAM_Arginosuc_synth_1kh3D03 (D:4-391)
1d: PFAM_Arginosuc_synth_1kh3D04 (D:4-391)
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Clan
:
HUP
(230)
Family
:
Arginosuc_synth
(8)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(3)
1a
Arginosuc_synth-1kh3D01
D:4-391
1b
Arginosuc_synth-1kh3D02
D:4-391
1c
Arginosuc_synth-1kh3D03
D:4-391
1d
Arginosuc_synth-1kh3D04
D:4-391
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Asym.Unit (269 KB)
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