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2ZSU
Biol. Unit 1
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Asym.Unit (288 KB)
Biol.Unit 1 (100 KB)
Biol.Unit 2 (96 KB)
Biol.Unit 3 (97 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM PYROCOCCUS HORIKOSHII OT3, P1 FORM
Authors
:
H. Mizutani, N. Kunishima
Date
:
17 Sep 08 (Deposition) - 21 Oct 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Spermidine Synthase, Aminopropylagmatine, Polyamine Biosynthesis, Spermidine Biosynthesis, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Mizutani, N. Kunishima
Crystal Structure Of Spermidine Synthase From Pyrococcus Horikoshii Ot3
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 1-{4-[(3-AMINOPROPYL)AMINO]BUTYL}G... (AG3a)
1b: 1-{4-[(3-AMINOPROPYL)AMINO]BUTYL}G... (AG3b)
1c: 1-{4-[(3-AMINOPROPYL)AMINO]BUTYL}G... (AG3c)
View:
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No.
Name
Count
Type
Full Name
1
AG3
1
Ligand/Ion
1-{4-[(3-AMINOPROPYL)AMINO]BUTYL}GUANIDINE
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:8 , TYR A:10 , VAL A:52 , GLN A:53 , TYR A:62 , HIS A:63 , ASP A:87 , ASP A:161 , SER A:162 , THR A:163 , ASP A:164 , TYR A:229 , TRP A:233
BINDING SITE FOR RESIDUE AG3 A1001
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PABS_2 (A:7-240,B:7-240)
2: PABS_1 (A:80-93,B:80-93)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PABS_2
PS51006
Polyamine biosynthesis (PABS) domain profile.
SPEE_PYRHO
7-240
2
A:7-240
B:7-240
-
-
-
-
2
PABS_1
PS01330
Polyamine biosynthesis (PABS) domain signature.
SPEE_PYRHO
80-93
2
A:80-93
B:80-93
-
-
-
-
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Exons
(0, 0)
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2zsua_ (A:)
1b: SCOP_d2zsub_ (B:)
1c: SCOP_d2zsuc_ (C:)
1d: SCOP_d2zsud_ (D:)
1e: SCOP_d2zsue_ (E:)
1f: SCOP_d2zsuf_ (F:)
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Protein Domains
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Organisms
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(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Superfamily
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Family
:
Spermidine synthase
(17)
Protein domain
:
automated matches
(5)
Pyrococcus horikoshii [TaxId: 53953]
(1)
1a
d2zsua_
A:
1b
d2zsub_
B:
1c
d2zsuc_
C:
1d
d2zsud_
D:
1e
d2zsue_
E:
1f
d2zsuf_
F:
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2zsuC02 (C:57-280)
1b: CATH_2zsuF02 (F:57-280)
1c: CATH_2zsuD02 (D:57-280)
1d: CATH_2zsuA02 (A:57-280)
1e: CATH_2zsuB02 (B:57-280)
1f: CATH_2zsuE02 (E:57-280)
2a: CATH_2zsuA01 (A:1-56)
2b: CATH_2zsuE01 (E:2-56)
2c: CATH_2zsuB01 (B:3-56)
2d: CATH_2zsuC01 (C:4-56)
2e: CATH_2zsuD01 (D:4-56)
2f: CATH_2zsuF01 (F:4-56)
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)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
Pyrococcus horikoshii. Organism_taxid: 53953. Strain: ot3.
(1)
1a
2zsuC02
C:57-280
1b
2zsuF02
F:57-280
1c
2zsuD02
D:57-280
1d
2zsuA02
A:57-280
1e
2zsuB02
B:57-280
1f
2zsuE02
E:57-280
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Spermidine Synthase; Chain: A, domain 2
(12)
Homologous Superfamily
:
[code=2.30.140.10, no name defined]
(9)
Pyrococcus horikoshii. Organism_taxid: 53953. Strain: ot3.
(1)
2a
2zsuA01
A:1-56
2b
2zsuE01
E:2-56
2c
2zsuB01
B:3-56
2d
2zsuC01
C:4-56
2e
2zsuD01
D:4-56
2f
2zsuF01
F:4-56
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Spermine_synth_2zsuF01 (F:4-252)
1b: PFAM_Spermine_synth_2zsuF02 (F:4-252)
1c: PFAM_Spermine_synth_2zsuF03 (F:4-252)
1d: PFAM_Spermine_synth_2zsuF04 (F:4-252)
1e: PFAM_Spermine_synth_2zsuF05 (F:4-252)
1f: PFAM_Spermine_synth_2zsuF06 (F:4-252)
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Clan
:
NADP_Rossmann
(1239)
Family
:
Spermine_synth
(12)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
(1)
1a
Spermine_synth-2zsuF01
F:4-252
1b
Spermine_synth-2zsuF02
F:4-252
1c
Spermine_synth-2zsuF03
F:4-252
1d
Spermine_synth-2zsuF04
F:4-252
1e
Spermine_synth-2zsuF05
F:4-252
1f
Spermine_synth-2zsuF06
F:4-252
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Asym.Unit (288 KB)
Header - Asym.Unit
Biol.Unit 1 (100 KB)
Header - Biol.Unit 1
Biol.Unit 2 (96 KB)
Header - Biol.Unit 2
Biol.Unit 3 (97 KB)
Header - Biol.Unit 3
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