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1UX6
Asym. Unit
Info
Asym.Unit (68 KB)
Biol.Unit 1 (61 KB)
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(1)
Title
:
STRUCTURE OF A THROMBOSPONDIN C-TERMINAL FRAGMENT REVEALS A NOVEL CALCIUM CORE IN THE TYPE 3 REPEATS
Authors
:
M. Kvansakul, J. C. Adams, E. Hohenester
Date
:
19 Feb 04 (Deposition) - 18 Mar 04 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Extracellular Matrix, Calcium Binding, L-Type Lectin, Glycoprotein, Cell Adhesion, Calcium-Binding, Heparin-Binding, Egf-Like Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kvansakul, J. C. Adams, E. Hohenester
Structure Of A Thrombospondin C-Terminal Fragment Reveals A Novel Calcium Core In The Type 3 Repeats
Embo J. V. 23 1223 2004
[
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Hetero Components
(1, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
16
Ligand/Ion
CALCIUM ION
[
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Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:917 , ASP A:919 , ASP A:926 , CYS A:928 , ASN A:931 , ILE A:934
BINDING SITE FOR RESIDUE CA B2001
02
AC2
SOFTWARE
ASP A:915 , ASP A:917 , ASP A:919 , VAL A:921 , ASP A:926 , HOH A:2154
BINDING SITE FOR RESIDUE CA B2002
03
AC3
SOFTWARE
ASP A:902 , ASP A:904 , ASP A:906 , ARG A:908 , HOH A:2239 , HOH A:2150
BINDING SITE FOR RESIDUE CA B2003
04
AC4
SOFTWARE
ASP A:879 , ASP A:881 , ASP A:883 , ILE A:885 , ASP A:890 , HOH A:2136
BINDING SITE FOR RESIDUE CA B2004
05
AC5
SOFTWARE
ASP A:881 , ASP A:883 , ASP A:890 , CYS A:892 , VAL A:895 , ASN A:897
BINDING SITE FOR RESIDUE CA B2005
06
AC6
SOFTWARE
ASP A:868 , ASP A:870 , ASP A:877 , ASP A:879 , ASN A:882 , HOH A:2294
BINDING SITE FOR RESIDUE CA B2006
07
AC7
SOFTWARE
ASP A:866 , ASP A:868 , ASP A:870 , LYS A:872 , ASP A:877 , HOH A:2118
BINDING SITE FOR RESIDUE CA B2007
08
AC8
SOFTWARE
ASP A:874 , ASP A:877 , ASP A:880 , ASP A:887 , HOH A:2280 , HOH A:2142
BINDING SITE FOR RESIDUE CA B2008
09
AC9
SOFTWARE
ASP A:845 , ASP A:847 , ASP A:854 , CYS A:856 , VAL A:859 , ASN A:861
BINDING SITE FOR RESIDUE CA B2009
10
BC1
SOFTWARE
ASP A:843 , ASP A:845 , ASP A:847 , HIS A:849 , ASP A:854 , HOH A:2122
BINDING SITE FOR RESIDUE CA B2010
11
BC2
SOFTWARE
ASP A:830 , ASP A:832 , ASP A:839 , ASN A:841 , HOH A:2241 , HOH A:2183
BINDING SITE FOR RESIDUE CA B2011
12
BC3
SOFTWARE
ASP A:828 , ASP A:830 , ASP A:832 , ILE A:834 , ASP A:839 , HOH A:2110
BINDING SITE FOR RESIDUE CA B2012
13
BC4
SOFTWARE
ASP A:825 , ASN A:973 , ASP A:1001 , ASP A:1003 , SER A:1136
BINDING SITE FOR RESIDUE CA B2013
14
BC5
SOFTWARE
GLU A:999 , ASP A:1001 , GLN A:1024 , ASP A:1086 , HOH A:2184 , HOH A:2244 , HOH A:2179
BINDING SITE FOR RESIDUE CA B2014
15
BC6
SOFTWARE
ASP A:825 , ASP A:1001 , ASP A:1002 , ASP A:1003 , GLN A:1027 , HOH A:2203
BINDING SITE FOR RESIDUE CA B2015
16
BC7
SOFTWARE
ASP A:948 , GLY A:951 , ASP A:956 , ASP A:975 , HOH A:2187 , HOH A:2149
BINDING SITE FOR RESIDUE CA B2016
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: TSP3 (-|-|-|-|-|A:827-864|A:865-900|A:90...)
2: TSP_CTER (A:940-1152)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TSP3
PS51234
Thrombospondin type-3 (TSP3) repeat profile.
TSP1_HUMAN
691-726
727-762
763-785
786-821
822-844
845-882
883-918
919-954
3
-
-
-
-
-
A:827-864
A:865-900
A:901-936
2
TSP_CTER
PS51236
Thrombospondin C-terminal domain profile.
TSP1_HUMAN
958-1170
1
A:940-1152
[
close PROSITE info
]
Exons
(7, 7)
Info
All Exons
Exon 1.16 (A:813-826)
Exon 1.17 (A:827-905)
Exon 1.18a (A:905-981 (gaps))
Exon 1.19a (A:981-1071)
Exon 1.19c (A:1072-1104)
Exon 1.20 (A:1104-1151)
Exon 1.21b (A:1151-1152)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.15/1.16
2: Boundary 1.16/1.17
3: Boundary 1.17/1.18a
4: Boundary 1.18a/1.19a
5: Boundary 1.19a/1.19c
6: Boundary 1.19c/1.20
7: Boundary 1.20/1.21b
8: Boundary 1.21b/-
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
ENST00000260356
1a
ENSE00001948740
chr15:
39873127-39873429
303
TSP1_HUMAN
-
0
0
-
-
1.2b
ENST00000260356
2b
ENSE00002162162
chr15:
39874030-39874125
96
TSP1_HUMAN
1-23
23
0
-
-
1.3b
ENST00000260356
3b
ENSE00001792284
chr15:
39874394-39874953
560
TSP1_HUMAN
23-209
187
0
-
-
1.4
ENST00000260356
4
ENSE00001758707
chr15:
39875818-39875893
76
TSP1_HUMAN
210-235
26
0
-
-
1.5
ENST00000260356
5
ENSE00001725099
chr15:
39876189-39876388
200
TSP1_HUMAN
235-301
67
0
-
-
1.6
ENST00000260356
6
ENSE00001706898
chr15:
39876501-39876623
123
TSP1_HUMAN
302-342
41
0
-
-
1.7
ENST00000260356
7
ENSE00001674053
chr15:
39877671-39877764
94
TSP1_HUMAN
343-374
32
0
-
-
1.8b
ENST00000260356
8b
ENSE00001738791
chr15:
39879548-39879721
174
TSP1_HUMAN
374-432
59
0
-
-
1.9a
ENST00000260356
9a
ENSE00001608072
chr15:
39880243-39880419
177
TSP1_HUMAN
432-491
60
0
-
-
1.10b
ENST00000260356
10b
ENSE00001783863
chr15:
39880727-39880900
174
TSP1_HUMAN
491-549
59
0
-
-
1.11c
ENST00000260356
11c
ENSE00001710663
chr15:
39881160-39881287
128
TSP1_HUMAN
549-591
43
0
-
-
1.12
ENST00000260356
12
ENSE00001794374
chr15:
39881403-39881555
153
TSP1_HUMAN
592-642
51
0
-
-
1.13c
ENST00000260356
13c
ENSE00000883769
chr15:
39882006-39882224
219
TSP1_HUMAN
643-715
73
0
-
-
1.14
ENST00000260356
14
ENSE00000883770
chr15:
39882717-39882824
108
TSP1_HUMAN
716-751
36
0
-
-
1.15
ENST00000260356
15
ENSE00000883771
chr15:
39883392-39883551
160
TSP1_HUMAN
752-805
54
0
-
-
1.16
ENST00000260356
16
ENSE00000883772
chr15:
39883706-39883824
119
TSP1_HUMAN
805-844
40
1
A:813-826
14
1.17
ENST00000260356
17
ENSE00000883773
chr15:
39884769-39885003
235
TSP1_HUMAN
845-923
79
1
A:827-905
79
1.18a
ENST00000260356
18a
ENSE00000883774
chr15:
39885201-39885428
228
TSP1_HUMAN
923-999
77
1
A:905-981 (gaps)
77
1.19a
ENST00000260356
19a
ENSE00000883775
chr15:
39885598-39885869
272
TSP1_HUMAN
999-1089
91
1
A:981-1071
91
1.19c
ENST00000260356
19c
ENSE00000883776
chr15:
39886300-39886397
98
TSP1_HUMAN
1090-1122
33
1
A:1072-1104
33
1.20
ENST00000260356
20
ENSE00000883777
chr15:
39886502-39886641
140
TSP1_HUMAN
1122-1169
48
1
A:1104-1151
48
1.21b
ENST00000260356
21b
ENSE00000930951
chr15:
39887563-39891119
3557
TSP1_HUMAN
1169-1170
2
1
A:1151-1152
2
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ux6a1 (A:937-1152)
2a: SCOP_d1ux6a2 (A:813-936)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Thrombospondin C-terminal domain
(1)
Protein domain
:
Thrombospondin C-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1ux6a1
A:937-1152
Class
:
Small proteins
(3458)
Fold
:
TSP type-3 repeat
(1)
Superfamily
:
TSP type-3 repeat
(1)
Family
:
TSP type-3 repeat
(1)
Protein domain
:
Thrombospondin-1
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1ux6a2
A:813-936
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1ux6A01 (A:813-939)
2a: CATH_1ux6A02 (A:940-1152)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
TSP type-3 repeat
(1)
Homologous Superfamily
:
TSP type-3 repeat
(1)
Human (Homo sapiens)
(1)
1a
1ux6A01
A:813-939
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Human (Homo sapiens)
(49)
2a
1ux6A02
A:940-1152
[
close CATH info
]
Pfam Domains
(2, 5)
Info
all PFAM domains
1a: PFAM_TSP_3_1ux6A01 (A:901-936)
1b: PFAM_TSP_3_1ux6A02 (A:901-936)
1c: PFAM_TSP_3_1ux6A03 (A:901-936)
1d: PFAM_TSP_3_1ux6A04 (A:901-936)
2a: PFAM_TSP_C_1ux6A05 (A:954-1152)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: TSP_3]
(3)
Family
:
TSP_3
(3)
Homo sapiens (Human)
(3)
1a
TSP_3-1ux6A01
A:901-936
1b
TSP_3-1ux6A02
A:901-936
1c
TSP_3-1ux6A03
A:901-936
1d
TSP_3-1ux6A04
A:901-936
Clan
:
no clan defined [family: TSP_C]
(3)
Family
:
TSP_C
(3)
Homo sapiens (Human)
(3)
2a
TSP_C-1ux6A05
A:954-1152
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Atom Selection
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Asymmetric Unit 1
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