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2P0A
Asym. Unit
Info
Asym.Unit (113 KB)
Biol.Unit 1 (208 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF HUMAN SYNAPSIN III (SYN3) IN COMPLEX WITH AMPPNP
Authors
:
A. P. Turnbull, C. Phillips, A. C. W. Pike, J. M. Elkins, C. Gileadi, E. Sa F. H. Niesen, N. Burgess, O. Gileadi, F. Gorrec, C. Umeano, F. Von Delf J. Weigelt, A. Edwards, C. H. Arrowsmith, M. Sundstrom, D. Doyle, Stru Genomics Consortium (Sgc)
Date
:
28 Feb 07 (Deposition) - 27 Mar 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Synapsin, Neurotransmitter Release, Schizophrenia, Vesicle Transport, Structural Genomics, Structural Genomics Consortium, Sgc, Neuropeptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. P. Turnbull, C. Phillips, A. C. W. Pike, J. M. Elkins, C. Gileadi, E. Salah, F. H. Niesen, N. Burgess, O. Gileadi, F. Gorrec, C. Umeano, F. Von Delft, J. Weigelt, A. Edwards, C. H. Arrowsmith, M. Sundstrom, D. Doyle
The Crystal Structure Of Human Synapsin Iii (Syn3) In Complex With Amppnp
To Be Published
[
close entry info
]
Hetero Components
(4, 18)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
CL
2
Ligand/Ion
CHLORIDE ION
3
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:170 , ALA A:172 , ALA A:252 , HIS A:253 , HOH A:745
BINDING SITE FOR RESIDUE CL A 501
02
AC2
SOFTWARE
SER B:170 , ALA B:172 , LEU B:173 , ALA B:252 , HIS B:253 , HOH B:740
BINDING SITE FOR RESIDUE CL B 501
03
AC3
SOFTWARE
ALA A:100 , ARG A:165 , PRO A:372 , LEU A:373 , ARG A:382 , EDO A:603 , HOH A:716 , HOH A:776 , HOH A:787 , HOH A:826 , HOH A:848
BINDING SITE FOR RESIDUE SO4 A 701
04
AC4
SOFTWARE
ARG A:294 , ARG A:307 , ASN A:317 , LYS A:352 , MET A:367 , PRO A:372 , ILE A:374 , ANP A:707 , HOH A:857
BINDING SITE FOR RESIDUE SO4 A 702
05
AC5
SOFTWARE
ARG B:165 , PRO B:372 , LEU B:373 , ARG B:382 , HOH B:730 , HOH B:779 , HOH B:815 , HOH B:903
BINDING SITE FOR RESIDUE SO4 B 703
06
AC6
SOFTWARE
ARG B:294 , ARG B:307 , ASN B:317 , LYS B:352 , MET B:367 , PRO B:372 , ILE B:374 , ANP B:705 , HOH B:907
BINDING SITE FOR RESIDUE SO4 B 704
07
AC7
SOFTWARE
GLU A:376 , HIS A:377 , GLU A:379 , GLU A:380 , HOH A:749
BINDING SITE FOR RESIDUE SO4 A 705
08
AC8
SOFTWARE
TYR A:169 , ARG A:178 , HOH A:770 , HOH A:785 , HOH A:831 , ARG B:178
BINDING SITE FOR RESIDUE SO4 A 706
09
AC9
SOFTWARE
LYS A:204 , LYS A:248 , ALA A:252 , HIS A:253 , ALA A:254 , GLY A:255 , LYS A:258 , GLU A:284 , ALA A:285 , ILE A:287 , ASP A:292 , TRP A:314 , LYS A:315 , ALA A:316 , ASN A:317 , LYS A:352 , ILE A:364 , GLU A:365 , SO4 A:702 , HOH A:713 , HOH A:754 , HOH A:889
BINDING SITE FOR RESIDUE ANP A 707
10
BC1
SOFTWARE
LYS B:204 , LYS B:248 , ALA B:252 , HIS B:253 , ALA B:254 , GLY B:255 , LYS B:258 , GLU B:284 , ALA B:285 , ILE B:287 , ASP B:292 , TRP B:314 , LYS B:315 , ALA B:316 , ASN B:317 , LYS B:352 , ILE B:364 , GLU B:365 , SO4 B:704 , HOH B:720 , HOH B:787 , HOH B:831 , HOH B:885 , HOH B:896
BINDING SITE FOR RESIDUE ANP B 705
11
BC2
SOFTWARE
VAL A:226 , GLU A:227 , TYR A:362 , EDO A:608 , HOH A:719
BINDING SITE FOR RESIDUE EDO A 601
12
BC3
SOFTWARE
ILE A:259 , LYS A:260 , VAL A:261 , GLU A:262 , ASP A:266 , HOH B:801
BINDING SITE FOR RESIDUE EDO A 602
13
BC4
SOFTWARE
ARG A:165 , HIS A:167 , SER A:370 , PRO A:372 , SO4 A:701 , HOH A:728 , HOH A:787
BINDING SITE FOR RESIDUE EDO A 603
14
BC5
SOFTWARE
ASP A:266 , ASP A:269 , LYS B:260 , TRP B:314 , HOH B:872
BINDING SITE FOR RESIDUE EDO A 604
15
BC6
SOFTWARE
PHE B:215 , LEU B:225 , TYR B:362 , EDO B:606 , HOH B:895
BINDING SITE FOR RESIDUE EDO B 605
16
BC7
SOFTWARE
VAL B:226 , GLU B:227 , TYR B:362 , EDO B:605 , HOH B:715 , HOH B:898
BINDING SITE FOR RESIDUE EDO B 606
17
BC8
SOFTWARE
LYS A:213 , GLN B:185 , TYR B:196 , HOH B:712 , HOH B:874
BINDING SITE FOR RESIDUE EDO B 607
18
BC9
SOFTWARE
PHE A:215 , LEU A:225 , GLU A:227 , TYR A:362 , EDO A:601
BINDING SITE FOR RESIDUE EDO A 608
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SYNAPSIN_2 (A:250-260,B:250-260)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SYNAPSIN_2
PS00416
Synapsins signature 2.
SYN3_HUMAN
250-260
2
A:250-260
B:250-260
[
close PROSITE info
]
Exons
(10, 20)
Info
All Exons
Exon 1.4a (A:90-104 | B:90-104)
Exon 1.5b (A:104-123 | B:104-123)
Exon 1.7a (A:124-144 | B:124-144)
Exon 1.8a (A:155-207 | B:155-207)
Exon 1.9a (A:208-237 | B:208-237)
Exon 1.11 (A:238-258 | B:238-258)
Exon 1.12 (A:259-306 | B:259-306)
Exon 1.13 (A:306-331 | B:306-331)
Exon 1.14 (A:331-365 | B:331-365)
Exon 1.16c (A:366-397 | B:366-397)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1/1.4a
02: Boundary 1.4a/1.5b
03: Boundary 1.5b/1.7a
04: Boundary 1.7a/1.8a
05: Boundary 1.8a/1.9a
06: Boundary 1.9a/1.11
07: Boundary 1.11/1.12
08: Boundary 1.12/1.13
09: Boundary 1.13/1.14
10: Boundary 1.14/1.16c
11: Boundary 1.16c/1.17
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
1.1
ENST00000358763
1
ENSE00001528638
chr22:
33454358-33454278
81
SYN3_HUMAN
-
0
0
-
-
1.4a
ENST00000358763
4a
ENSE00001528637
chr22:
33402809-33402337
473
SYN3_HUMAN
1-104
104
2
A:90-104
B:90-104
15
15
1.5b
ENST00000358763
5b
ENSE00002150303
chr22:
33376687-33376630
58
SYN3_HUMAN
104-123
20
2
A:104-123
B:104-123
20
20
1.7a
ENST00000358763
7a
ENSE00001324487
chr22:
33327466-33327375
92
SYN3_HUMAN
124-154
31
2
A:124-144
B:124-144
21
21
1.8a
ENST00000358763
8a
ENSE00001304263
chr22:
33265112-33264953
160
SYN3_HUMAN
154-207
54
2
A:155-207
B:155-207
53
53
1.9a
ENST00000358763
9a
ENSE00001315144
chr22:
33260991-33260902
90
SYN3_HUMAN
208-237
30
2
A:208-237
B:208-237
30
30
1.11
ENST00000358763
11
ENSE00001292222
chr22:
32992722-32992660
63
SYN3_HUMAN
238-258
21
2
A:238-258
B:238-258
21
21
1.12
ENST00000358763
12
ENSE00001315501
chr22:
32937699-32937557
143
SYN3_HUMAN
259-306
48
2
A:259-306
B:259-306
48
48
1.13
ENST00000358763
13
ENSE00001602975
chr22:
32934096-32934022
75
SYN3_HUMAN
306-331
26
2
A:306-331
B:306-331
26
26
1.14
ENST00000358763
14
ENSE00001781645
chr22:
32929881-32929779
103
SYN3_HUMAN
331-365
35
2
A:331-365
B:331-365
35
35
1.16c
ENST00000358763
16c
ENSE00001671976
chr22:
32924995-32924861
135
SYN3_HUMAN
366-410
45
2
A:366-397
B:366-397
32
32
1.17
ENST00000358763
17
ENSE00001307135
chr22:
32923992-32923905
88
SYN3_HUMAN
411-440
30
0
-
-
1.19d
ENST00000358763
19d
ENSE00001294261
chr22:
32914321-32914030
292
SYN3_HUMAN
440-537
98
0
-
-
1.21f
ENST00000358763
21f
ENSE00001528635
chr22:
32909811-32908539
1273
SYN3_HUMAN
537-580
44
0
-
-
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2p0aa2 (A:193-397)
1b: SCOP_d2p0ab2 (B:193-397)
2a: SCOP_d2p0aa1 (A:90-192)
2b: SCOP_d2p0ab1 (B:90-192)
View:
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)
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(
)
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(
)
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)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
Synapsin C-terminal domain
(7)
Protein domain
:
automated matches
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2p0aa2
A:193-397
1b
d2p0ab2
B:193-397
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
automated matches
(45)
Protein domain
:
automated matches
(45)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2p0aa1
A:90-192
2b
d2p0ab1
B:90-192
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2p0aA02 (A:194-226,A:287-372)
1b: CATH_2p0aB02 (B:194-226,B:287-372)
2a: CATH_2p0aA03 (A:227-286)
2b: CATH_2p0aB03 (B:227-286)
3a: CATH_2p0aA01 (A:90-193,A:373-385)
3b: CATH_2p0aB01 (B:90-193,B:373-385)
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(
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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)
Human (Homo sapiens)
(3)
1a
2p0aA02
A:194-226,A:287-372
1b
2p0aB02
B:194-226,B:287-372
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Human (Homo sapiens)
(3)
2a
2p0aA03
A:227-286
2b
2p0aB03
B:227-286
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.20, no name defined]
(85)
Human (Homo sapiens)
(2)
3a
2p0aA01
A:90-193,A:373-385
3b
2p0aB01
B:90-193,B:373-385
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Synapsin_C_2p0aB01 (B:193-395)
1b: PFAM_Synapsin_C_2p0aB02 (B:193-395)
2a: PFAM_Synapsin_2p0aB03 (B:90-191)
2b: PFAM_Synapsin_2p0aB04 (B:90-191)
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Clans
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Organisms
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(
)
Clan
:
ATP-grasp
(83)
Family
:
Synapsin_C
(3)
Homo sapiens (Human)
(1)
1a
Synapsin_C-2p0aB01
B:193-395
1b
Synapsin_C-2p0aB02
B:193-395
Clan
:
no clan defined [family: Synapsin]
(3)
Family
:
Synapsin
(3)
Homo sapiens (Human)
(1)
2a
Synapsin-2p0aB03
B:90-191
2b
Synapsin-2p0aB04
B:90-191
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