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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'Exon' information from database.
2O07
Asym. Unit
Info
Asym.Unit (108 KB)
Biol.Unit 1 (103 KB)
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(1)
Title
:
HUMAN SPERMIDINE SYNTHASE
Authors
:
J. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date
:
27 Nov 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.89
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Spermidine Synthase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Wu, J. Min, Y. Ikeguchi, H. Zeng, A. Dong, P. Loppnau, A. E. Pegg, A. N. Plotnikov
Structure And Mechanism Of Spermidine Synthases.
Biochemistry V. 46 8331 2007
(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)
2a: SPERMIDINE (SPDa)
2b: SPERMIDINE (SPDb)
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: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:23 , VAL A:68 , ILE A:69 , GLN A:70 , TYR A:79 , GLN A:80 , ASP A:104 , ASP A:173 , SER A:174 , TYR A:241 , PRO A:242 , MTA A:501
BINDING SITE FOR RESIDUE SPD A 601
2
AC2
SOFTWARE
TRP B:28 , VAL B:68 , GLN B:70 , TYR B:79 , GLN B:80 , ASP B:104 , ASP B:173 , SER B:174 , ASP B:176 , TYR B:241 , MTA B:501 , HOH B:603 , HOH B:605
BINDING SITE FOR RESIDUE SPD B 601
3
AC3
SOFTWARE
GLN A:49 , LEU A:65 , GLY A:101 , GLY A:103 , ASP A:104 , CYS A:123 , GLU A:124 , ILE A:125 , VAL A:129 , GLY A:154 , ASP A:155 , GLY A:156 , ASP A:173 , SER A:175 , SPD A:601
BINDING SITE FOR RESIDUE MTA A 501
4
AC4
SOFTWARE
GLN B:49 , LEU B:65 , GLY B:101 , GLY B:103 , ASP B:104 , CYS B:123 , GLU B:124 , ILE B:125 , ASP B:126 , VAL B:129 , GLY B:154 , ASP B:155 , GLY B:156 , ASP B:173 , PRO B:180 , ALA B:181 , SER B:183 , SPD B:601
BINDING SITE FOR RESIDUE MTA B 501
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011807 (L149V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011807
L
149
V
SPEE_HUMAN
Polymorphism
1049932
A/B
L
149
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PABS_2 (A:18-253,B:18-253)
2: PABS_1 (A:97-110,B:97-110)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PABS_2
PS51006
Polyamine biosynthesis (PABS) domain profile.
SPEE_HUMAN
18-253
2
A:18-253
B:18-253
2
PABS_1
PS01330
Polyamine biosynthesis (PABS) domain signature.
SPEE_HUMAN
97-110
2
A:97-110
B:97-110
[
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]
Exons
(8, 16)
Info
All Exons
Exon 1.1a (A:16-56 | B:15-56)
Exon 1.2c (A:56-96 | B:56-96)
Exon 1.3a (A:97-127 | B:97-127)
Exon 1.4b (A:128-175 | B:128-179)
Exon 1.5 (A:187-207 | B:179-207)
Exon 1.6b (A:207-255 | B:207-255)
Exon 1.7b (A:256-296 | B:256-296)
Exon 1.7d (A:297-300 | B:297-299)
View:
Select:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2c
3: Boundary 1.2c/1.3a
4: Boundary 1.3a/1.4b
5: Boundary 1.4b/1.5
6: Boundary 1.5/1.6b
7: Boundary 1.6b/1.7b
8: Boundary 1.7b/1.7d
9: Boundary 1.7d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000376957
1a
ENSE00001836529
chr1:
11120081-11119834
248
SPEE_HUMAN
1-56
56
2
A:16-56
B:15-56
41
42
1.2c
ENST00000376957
2c
ENSE00000743131
chr1:
11119402-11119282
121
SPEE_HUMAN
56-96
41
2
A:56-96
B:56-96
41
41
1.3a
ENST00000376957
3a
ENSE00000743128
chr1:
11118949-11118857
93
SPEE_HUMAN
97-127
31
2
A:97-127
B:97-127
31
31
1.4b
ENST00000376957
4b
ENSE00000743127
chr1:
11116814-11116661
154
SPEE_HUMAN
128-179
52
2
A:128-175
B:128-179
48
52
1.5
ENST00000376957
5
ENSE00000743125
chr1:
11116151-11116068
84
SPEE_HUMAN
179-207
29
2
A:187-207
B:179-207
21
29
1.6b
ENST00000376957
6b
ENSE00000743124
chr1:
11115983-11115838
146
SPEE_HUMAN
207-255
49
2
A:207-255
B:207-255
49
49
1.7b
ENST00000376957
7b
ENSE00000743123
chr1:
11115141-11115019
123
SPEE_HUMAN
256-296
41
2
A:256-296
B:256-296
41
41
1.7d
ENST00000376957
7d
ENSE00001847545
chr1:
11114942-11114646
297
SPEE_HUMAN
297-302
6
2
A:297-300
B:297-299
4
3
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2o07a_ (A:)
1b: SCOP_d2o07b_ (B:)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
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
:
Spermidine synthase
(11)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d2o07a_
A:
1b
d2o07b_
B:
[
close SCOP info
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2o07B02 (B:75-299)
1b: CATH_2o07A02 (A:75-300)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
Human (Homo sapiens)
(49)
1a
2o07B02
B:75-299
1b
2o07A02
A:75-300
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (108 KB)
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