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5GJE
Asym. Unit
Info
Asym.Unit (337 KB)
Biol.Unit 1 (331 KB)
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(1)
Title
:
THREE-DIMENSIONAL RECONSTRUCTION OF HUMAN LRP6 ECTODOMAIN COMPLEXED WITH DKK1
Authors
:
K. Matoba, E. Mihara, K. Tamura-Kawakami, H. Hirai, S. Thompson, K. Iwa J. Takagi
Date
:
29 Jun 16 (Deposition) - 18 Jan 17 (Release) - 18 Jan 17 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
21.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Wnt Signaling, Wnt Co-Receptor, Lrp6, Glycoprotein, Antagonist, Dkk1, Conformational Change, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Matoba, E. Mihara, K. Tamura-Kawakami, N. Miyazaki, S. Maeda, H. Hirai, S. Thompson, K. Iwasaki, J. Takagi
Conformational Freedom Of The Lrp6 Ectodomain Is Regulated By N-Glycosylation And The Binding Of The Wnt Antagonist Dkk1
Cell Rep V. 18 32 2017
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Hetero Components
(4, 17)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
2a: GLYCEROL (GOLa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
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No.
Name
Count
Type
Full Name
1
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
2
GOL
1
Ligand/Ion
GLYCEROL
3
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
PO4
2
Ligand/Ion
PHOSPHATE ION
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Sites
(11, 11)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:169 , THR A:212 , HIS A:253 , ARG A:259
binding site for residue PO4 A 707
02
AC2
SOFTWARE
ARG A:396 , LEU A:413 , NAG A:705
binding site for residue PO4 A 708
03
AC3
SOFTWARE
ARG B:985
binding site for residue GOL B 1309
04
AC4
SOFTWARE
ASN A:262 , ALA A:263 , THR A:264
binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 262
05
AC5
SOFTWARE
ARG A:412 , ASN A:414 , PO4 A:708 , HOH A:801
binding site for Poly-Saccharide residues NAG A 705 through NAG A 706 bound to ASN A 414
06
AC6
SOFTWARE
VAL A:464 , ASN A:467
binding site for Poly-Saccharide residues NAG A 703 through NAG A 704 bound to ASN A 467
07
AC7
SOFTWARE
ASN B:674 , PHE B:690 , ASN B:692
binding site for Poly-Saccharide residues NAG B 1301 through FUC B 1303 bound to ASN B 692
08
AC8
SOFTWARE
ASP B:843 , ASN B:859 , THR B:861 , SER B:862 , NAG B:1305
binding site for Mono-Saccharide NAG B 1304 bound to ASN B 859
09
AC9
SOFTWARE
ASN B:865 , NAG B:1304
binding site for Mono-Saccharide NAG B 1305 bound to ASN B 865
10
AD1
SOFTWARE
ALA B:924 , ASN B:926
binding site for Mono-Saccharide NAG B 1306 bound to ASN B 926
11
AD2
SOFTWARE
TRP B:1030 , ASN B:1039 , THR B:1041 , GLY B:1045 , SER B:1047 , VAL B:1050
binding site for Poly-Saccharide residues NAG B 1307 through NAG B 1308 bound to ASN B 1039
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (337 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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