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Biol. Unit 1
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Asym.Unit (83 KB)
Biol.Unit 1 (40 KB)
Biol.Unit 2 (40 KB)
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(1)
Title
:
HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR
Authors
:
E. Hohenester, T. Sasaki, R. Timpl
Date
:
05 Dec 97 (Deposition) - 30 Dec 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Extracellular Module, Glycoprotein, Anti-Adhesive Protein, Collagen Binding, Site-Directed Mutagenesis, Glycosylated Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Sasaki, E. Hohenester, W. Gohring, R. Timpl
Crystal Structure And Mapping By Site-Directed Mutagenesis Of The Collagen-Binding Epitope Of An Activated Form Of Bm-40/Sparc/Osteonectin.
Embo J. V. 17 1625 1998
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
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)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:99 , CYS A:132 , LYS A:133 , TYR A:134 , NAG A:402
BINDING SITE FOR RESIDUE NAG A 401
2
AC2
SOFTWARE
CYS A:132 , LYS A:133 , NAG A:401
BINDING SITE FOR RESIDUE NAG A 402
3
AC5
SOFTWARE
ASP A:222 , PRO A:225 , ASP A:227 , TYR A:229 , GLU A:234
BINDING SITE FOR RESIDUE CA A 301
4
AC6
SOFTWARE
ASP A:257 , ASP A:259 , ASP A:261 , TYR A:263 , GLU A:268
BINDING SITE FOR RESIDUE CA A 302
5
AC7
SOFTWARE
PRO A:241 , ILE A:243 , GLU A:246 , THR B:160 , GLU B:163
BINDING SITE FOR RESIDUE CA A 303
6
BC1
SOFTWARE
THR A:160 , GLU A:163 , PRO B:241 , ILE B:243 , GLU B:246
BINDING SITE FOR RESIDUE CA B 303
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_059530 (A53S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_059530
N
70
S
SPRC_HUMAN
Polymorphism
13359508
A
A
53
S
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:
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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
(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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1nuba1 (A:136-286)
1b: SCOP_d1nubb1 (B:136-286)
2a: SCOP_d1nuba3 (A:78-135)
2b: SCOP_d1nubb3 (B:78-135)
3a: SCOP_d1nuba2 (A:53-77)
3b: SCOP_d1nubb2 (B:53-77)
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)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Osteonectin
(3)
Protein domain
:
C-terminal (EC) domain of BM-40/SPARC/osteonectin
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1nuba1
A:136-286
1b
d1nubb1
B:136-286
Class
:
Small proteins
(3458)
Fold
:
Kazal-type serine protease inhibitors
(75)
Superfamily
:
Kazal-type serine protease inhibitors
(75)
Family
:
Ovomucoid domain III-like
(69)
Protein domain
:
Domain of BM-40/SPARC/osteonectin
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d1nuba3
A:78-135
2b
d1nubb3
B:78-135
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
Follistatin (FS) module N-terminal domain, FS-N
(5)
Protein domain
:
Domain of BM-40/SPARC/osteonectin
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
3a
d1nuba2
A:53-77
3b
d1nubb2
B:53-77
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1nubA01 (A:53-134)
1b: CATH_1nubB01 (B:53-134)
2a: CATH_1nubA02 (A:135-286)
2b: CATH_1nubB02 (B:135-286)
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)
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)
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(
)
(
)
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
1nubA01
A:53-134
1b
1nubB01
B:53-134
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Human (Homo sapiens)
(106)
2a
1nubA02
A:135-286
2b
1nubB02
B:135-286
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_SPARC_Ca_bdg_1nubB01 (B:135-272)
1b: PFAM_SPARC_Ca_bdg_1nubB02 (B:135-272)
2a: PFAM_FOLN_1nubB03 (B:55-76)
2b: PFAM_FOLN_1nubB04 (B:55-76)
3a: PFAM_Kazal_1_1nubB05 (B:78-132)
3b: PFAM_Kazal_1_1nubB06 (B:78-132)
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Clans
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)
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)
(
)
Organisms
(
)
(
)
Clan
:
EF_hand
(270)
Family
:
SPARC_Ca_bdg
(3)
Homo sapiens (Human)
(3)
1a
SPARC_Ca_bdg-1nubB01
B:135-272
1b
SPARC_Ca_bdg-1nubB02
B:135-272
Clan
:
EGF
(60)
Family
:
FOLN
(6)
Homo sapiens (Human)
(4)
2a
FOLN-1nubB03
B:55-76
2b
FOLN-1nubB04
B:55-76
Clan
:
Kazal
(46)
Family
:
Kazal_1
(34)
Homo sapiens (Human)
(6)
3a
Kazal_1-1nubB05
B:78-132
3b
Kazal_1-1nubB06
B:78-132
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Asym.Unit (83 KB)
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