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3C6K
Biol. Unit 2
Info
Asym.Unit (254 KB)
Biol.Unit 1 (125 KB)
Biol.Unit 2 (127 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN SPERMINE SYNTHASE IN COMPLEX WITH SPERMIDINE AND 5-METHYLTHIOADENOSINE
Authors
:
J. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. E. Pegg, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date
:
04 Feb 08 (Deposition) - 19 Feb 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Spermidine Aminopropyltransferase, Spmsy, Structural Genomics, Structural Genomics Consortium, Sgc, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Wu, J. Min, H. Zeng, D. E. Mccloskey, Y. Ikeguchi, P. Loppnau, A. J. Michael, A. E. Pegg, A. N. Plotnikov
Crystal Structure Of Human Spermine Synthase: Implications Of Substrate Binding And Catalytic Mechanism.
J. Biol. Chem. V. 283 16135 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTAa)
1b: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTAb)
1c: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTAc)
1d: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTAd)
2a: SPERMIDINE (SPDa)
2b: SPERMIDINE (SPDb)
2c: SPERMIDINE (SPDc)
2d: SPERMIDINE (SPDd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MTA
2
Ligand/Ion
5'-DEOXY-5'-METHYLTHIOADENOSINE
2
SPD
2
Ligand/Ion
SPERMIDINE
[
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Sites
(4, 4)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
ASP C:169 , VAL C:170 , ASN C:171 , TYR C:179 , ASP C:278 , LEU C:279 , TYR C:353 , GLU C:355 , TRP C:357 , HOH C:752 , HOH C:778
BINDING SITE FOR RESIDUE SPD C 501
2
AC4
SOFTWARE
ASP D:169 , VAL D:170 , ASN D:171 , TYR D:179 , ASP D:278 , LEU D:279 , TYR D:353 , GLU D:355 , TRP D:357 , HOH D:687 , HOH D:689 , HOH D:692
BINDING SITE FOR RESIDUE SPD D 501
3
AC7
SOFTWARE
GLN C:150 , LEU C:164 , LEU C:166 , GLY C:200 , VAL C:221 , GLU C:222 , ILE C:223 , ASP C:224 , VAL C:227 , ASP C:257 , CYS C:258 , ASP C:278 , LEU C:279 , THR C:280 , ILE C:284
BINDING SITE FOR RESIDUE MTA C 401
4
AC8
SOFTWARE
GLN D:150 , LEU D:164 , LEU D:166 , ASN D:171 , GLY D:200 , GLY D:202 , VAL D:221 , GLU D:222 , ILE D:223 , VAL D:227 , ASP D:257 , CYS D:258 , ASP D:278 , LEU D:279 , THR D:280 , ILE D:284
BINDING SITE FOR RESIDUE MTA D 401
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_072748 (F60L, chain C/D, )
2: VAR_071048 (N62S, chain C/D, )
View:
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_072748
F
58
L
SPSY_HUMAN
Disease (MRXSSR)
---
C/D
F
60
L
2
UniProt
VAR_071048
N
60
S
SPSY_HUMAN
Polymorphism
---
C/D
N
62
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PABS_2 (C:124-364,D:124-364)
2: PABS_1 (C:196-209,D:196-209)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PABS_2
PS51006
Polyamine biosynthesis (PABS) domain profile.
SPSY_HUMAN
122-362
2
-
-
C:124-364
D:124-364
2
PABS_1
PS01330
Polyamine biosynthesis (PABS) domain signature.
SPSY_HUMAN
194-207
2
-
-
C:196-209
D:196-209
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
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CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_3c6kA01 (A:5-118)
1b: CATH_3c6kB01 (B:6-118)
1c: CATH_3c6kC01 (C:5-118)
1d: CATH_3c6kD01 (D:5-118)
2a: CATH_3c6kB03 (B:175-368)
2b: CATH_3c6kD03 (D:175-367)
2c: CATH_3c6kC03 (C:175-368)
2d: CATH_3c6kA03 (A:175-367)
3a: CATH_3c6kA02 (A:119-174)
3b: CATH_3c6kB02 (B:119-174)
3c: CATH_3c6kC02 (C:119-174)
3d: CATH_3c6kD02 (D:119-174)
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Classes
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)
(
)
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(
)
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(
)
(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Double Stranded RNA Binding Domain
(204)
Homologous Superfamily
:
Siroheme synthase; domain 2
(6)
Human (Homo sapiens)
(2)
1a
3c6kA01
A:5-118
1b
3c6kB01
B:6-118
1c
3c6kC01
C:5-118
1d
3c6kD01
D:5-118
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
Human (Homo sapiens)
(49)
2a
3c6kB03
B:175-368
2b
3c6kD03
D:175-367
2c
3c6kC03
C:175-368
2d
3c6kA03
A:175-367
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)
Human (Homo sapiens)
(2)
3a
3c6kA02
A:119-174
3b
3c6kB02
B:119-174
3c
3c6kC02
C:119-174
3d
3c6kD02
D:119-174
[
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (254 KB)
Header - Asym.Unit
Biol.Unit 1 (125 KB)
Header - Biol.Unit 1
Biol.Unit 2 (127 KB)
Header - Biol.Unit 2
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