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2V53
Asym. Unit
Info
Asym.Unit (110 KB)
Biol.Unit 1 (102 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A SPARC-COLLAGEN COMPLEX
Authors
:
E. Hohenester, T. Sasaki, C. Giudici, R. W. Farndale, H. P. Bachinger
Date
:
01 Oct 08 (Deposition) - 25 Nov 08 (Release) - 09 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Glycosylated Protein, Cell Adhesion, Glycoprotein, Ionic Channel, Ion Transport, Copper, Calcium, Secreted, Collagen, Transport, Basement Membrane, Extracellular Matrix
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Hohenester, T. Sasaki, C. Giudici, R. W. Farndale, H. P. Bachinger
Structural Basis Of Sequence-Specific Collagen Recognition By Sparc.
Proc. Natl. Acad. Sci. Usa V. 105 18273 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 25)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: 4-HYDROXYPROLINE (HYPa)
2b: 4-HYDROXYPROLINE (HYPb)
2c: 4-HYDROXYPROLINE (HYPc)
2d: 4-HYDROXYPROLINE (HYPd)
2e: 4-HYDROXYPROLINE (HYPe)
2f: 4-HYDROXYPROLINE (HYPf)
2g: 4-HYDROXYPROLINE (HYPg)
2h: 4-HYDROXYPROLINE (HYPh)
2i: 4-HYDROXYPROLINE (HYPi)
2j: 4-HYDROXYPROLINE (HYPj)
2k: 4-HYDROXYPROLINE (HYPk)
2l: 4-HYDROXYPROLINE (HYPl)
2m: 4-HYDROXYPROLINE (HYPm)
2n: 4-HYDROXYPROLINE (HYPn)
2o: 4-HYDROXYPROLINE (HYPo)
2p: 4-HYDROXYPROLINE (HYPp)
2q: 4-HYDROXYPROLINE (HYPq)
2r: 4-HYDROXYPROLINE (HYPr)
2s: 4-HYDROXYPROLINE (HYPs)
2t: 4-HYDROXYPROLINE (HYPt)
2u: 4-HYDROXYPROLINE (HYPu)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
HYP
21
Mod. Amino Acid
4-HYDROXYPROLINE
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
1
Ligand/Ion
SULFATE ION
[
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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
ASP A:222 , PRO A:225 , ASP A:227 , TYR A:229 , GLU A:234
BINDING SITE FOR RESIDUE CA A 301
2
AC2
SOFTWARE
ASN A:99 , CYS A:132 , NAG A:402
BINDING SITE FOR RESIDUE NAG A 401
3
AC3
SOFTWARE
LYS A:133 , TYR A:134 , NAG A:401
BINDING SITE FOR RESIDUE NAG A 402
4
AC4
SOFTWARE
PRO C:26 , GLY D:13 , PRO D:14 , ARG D:15
BINDING SITE FOR RESIDUE SO4 D 401
[
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]
SAPs(SNPs)/Variants
(4, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011122 (G4E, chain B/C/D, )
2: VAR_001773 (G10E, chain B/C/D, )
3: VAR_001774 (G25S, chain B/C/D, )
4: VAR_001775 (P33T, chain B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011122
G
552
E
CO3A1_HUMAN
Disease (EDS4)
---
B/C/D
G
4
E
2
UniProt
VAR_001773
G
567
E
CO3A1_HUMAN
Disease (EDS4)
---
B/C/D
G
10
E
3
UniProt
VAR_001774
G
582
S
CO3A1_HUMAN
Disease (EDS4)
---
B/C/D
G
25
S
4
UniProt
VAR_001775
P
602
T
CO3A1_HUMAN
Polymorphism
35795890
B/C/D
P
33
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: OSTEONECTIN_1 (A:55-85)
2: KAZAL_2 (A:77-134)
3: OSTEONECTIN_2 (A:146-156)
4: EF_HAND_1 (A:257-269)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
OSTEONECTIN_1
PS00612
Osteonectin domain signature 1.
SPRC_HUMAN
72-102
1
A:55-85
2
KAZAL_2
PS51465
Kazal domain profile.
SPRC_HUMAN
94-151
1
A:77-134
3
OSTEONECTIN_2
PS00613
Osteonectin domain signature 2.
SPRC_HUMAN
163-173
1
A:146-156
4
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
SPRC_HUMAN
274-286
1
A:257-269
[
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]
Exons
(6, 6)
Info
All Exons
Exon 1.6b (A:54-93)
Exon 1.7 (A:94-134)
Exon 1.8c (A:134-178)
Exon 1.9b (A:179-228 (gaps))
Exon 1.10 (A:228-278)
Exon 1.11b (A:278-286)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5b/1.6b
2: Boundary 1.6b/1.7
3: Boundary 1.7/1.8c
4: Boundary 1.8c/1.9b
5: Boundary 1.9b/1.10
6: Boundary 1.10/1.11b
7: Boundary 1.11b/-
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
ENST00000231061
1a
ENSE00001218290
chr5:
151066726-151066426
301
SPRC_HUMAN
-
0
0
-
-
1.3
ENST00000231061
3
ENSE00002171871
chr5:
151055762-151055693
70
SPRC_HUMAN
1-19
19
0
-
-
1.4
ENST00000231061
4
ENSE00000767880
chr5:
151054235-151054173
63
SPRC_HUMAN
20-40
21
0
-
-
1.5b
ENST00000231061
5b
ENSE00000767879
chr5:
151052777-151052690
88
SPRC_HUMAN
41-70
30
0
-
-
1.6b
ENST00000231061
6b
ENSE00000841273
chr5:
151051255-151051134
122
SPRC_HUMAN
70-110
41
1
A:54-93
40
1.7
ENST00000231061
7
ENSE00000841272
chr5:
151049345-151049225
121
SPRC_HUMAN
111-151
41
1
A:94-134
41
1.8c
ENST00000231061
8c
ENSE00000841271
chr5:
151047161-151047028
134
SPRC_HUMAN
151-195
45
1
A:134-178
45
1.9b
ENST00000231061
9b
ENSE00000841270
chr5:
151046070-151045922
149
SPRC_HUMAN
196-245
50
1
A:179-228 (gaps)
50
1.10
ENST00000231061
10
ENSE00000841269
chr5:
151043796-151043648
149
SPRC_HUMAN
245-295
51
1
A:228-278
51
1.11b
ENST00000231061
11b
ENSE00001023043
chr5:
151043160-151040657
2504
SPRC_HUMAN
295-303
9
1
A:278-286
9
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2v53A01 (A:54-134)
2a: CATH_2v53A02 (A:135-286)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Wheat Germ Agglutinin (Isolectin 2); domain 1
(140)
Homologous Superfamily
:
[code=3.30.60.30, no name defined]
(93)
Human (Homo sapiens)
(13)
1a
2v53A01
A:54-134
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Human (Homo sapiens)
(106)
2a
2v53A02
A:135-286
[
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]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_SPARC_Ca_bdg_2v53A01 (A:135-272)
2a: PFAM_FOLN_2v53A02 (A:55-76)
3a: PFAM_Kazal_1_2v53A03 (A:78-132)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EF_hand
(270)
Family
:
SPARC_Ca_bdg
(3)
Homo sapiens (Human)
(3)
1a
SPARC_Ca_bdg-2v53A01
A:135-272
Clan
:
EGF
(60)
Family
:
FOLN
(6)
Homo sapiens (Human)
(4)
2a
FOLN-2v53A02
A:55-76
Clan
:
Kazal
(46)
Family
:
Kazal_1
(34)
Homo sapiens (Human)
(6)
3a
Kazal_1-2v53A03
A:78-132
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]
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