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3VYK
Asym. Unit
Info
Asym.Unit (32 KB)
Biol.Unit 1 (26 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF C-TYPE LECTIN DOMAIN OF MURINE DENDRITIC CELL INHIBITORY RECEPTOR 2 IN COMPLEX WITH N-GLYCAN
Authors
:
M. Nagae, K. Yamanaka, S. Hanashima, A. Ikeda, T. Satoh, N. Matsumoto, K. Yamamoto, Y. Yamaguchi
Date
:
26 Sep 12 (Deposition) - 02 Oct 13 (Release) - 11 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
C-Type Lectin Fold, Cell Surface, Carbohydrate Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Nagae, K. Yamanaka, S. Hanashima, A. Ikeda, K. Morita-Matsumoto, T. Satoh, N. Matsumoto, K. Yamamoto, Y. Yamaguchi
Recognition Of Bisecting N-Acetylglucosamine: Structural Basis For Asymmetric Interaction With The Mouse Lectin Dendritic Cell Inhibitory Receptor 2
J. Biol. Chem. V. 288 33598 2013
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Hetero Components
(6, 10)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: 1,2-ETHANEDIOL (EDOa)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
4a: O1-METHYL-MANNOSE (MMAa)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
4
MMA
1
Ligand/Ion
O1-METHYL-MANNOSE
5
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SO4
2
Ligand/Ion
SULFATE ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:196 , ASN A:198 , GLU A:202 , ASN A:217 , ASP A:218 , MAN A:1002
BINDING SITE FOR RESIDUE CA A 1007
2
AC2
SOFTWARE
VAL A:115 , SER A:148 , GLN A:149 , ALA A:150 , ARG A:203 , LYS A:222 , HOH A:1148 , HOH A:1149
BINDING SITE FOR RESIDUE SO4 A 1008
3
AC3
SOFTWARE
SER A:106 , PRO A:113 , GLY A:213 , TRP A:214 , HOH A:1127 , HOH A:1178 , HOH A:1179
BINDING SITE FOR RESIDUE SO4 A 1009
4
AC4
SOFTWARE
MAN A:1004 , NAG A:1005 , NAG A:1006
BINDING SITE FOR RESIDUE EDO A 1010
5
AC5
SOFTWARE
THR A:183 , GLU A:196 , ASN A:198 , TRP A:201 , GLU A:202 , ASN A:208 , ASN A:217 , ASP A:218 , ILE A:219 , PRO A:220 , ASP A:223 , HIS A:225 , LYS A:232 , CA A:1007 , EDO A:1010 , HOH A:1130 , HOH A:1131 , HOH A:1134 , HOH A:1136 , HOH A:1155 , HOH A:1156 , HOH A:1166 , HOH A:1167
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1001 TO 1006
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(3, 3)
Info
All Exons
Exon 1.4 (A:106-152)
Exon 1.5 (A:153-190)
Exon 1.6 (A:190-233)
View:
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All Exon Boundaries
1: Boundary 1.3/1.4
2: Boundary 1.4/1.5
3: Boundary 1.5/1.6
4: Boundary 1.6/-
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
ENSMUST00000079379
1
ENSMUSE00000520646
chr6:
122940385-122940466
82
Q5YIR8_MOUSE
1-28
28
0
-
-
1.2
ENSMUST00000079379
2
ENSMUSE00000463896
chr6:
122941778-122941894
117
Q5YIR8_MOUSE
28-67
40
0
-
-
1.3
ENSMUST00000079379
3
ENSMUSE00000464662
chr6:
122954027-122954128
102
Q5YIR8_MOUSE
67-101
35
0
-
-
1.4
ENSMUST00000079379
4
ENSMUSE00000552557
chr6:
122962721-122962875
155
Q5YIR8_MOUSE
101-152
52
1
A:106-152
47
1.5
ENSMUST00000079379
5
ENSMUSE00000552554
chr6:
122963777-122963889
113
Q5YIR8_MOUSE
153-190
38
1
A:153-190
38
1.6
ENSMUST00000079379
6
ENSMUSE00000504342
chr6:
122973917-122974123
207
Q5YIR8_MOUSE
190-236
47
1
A:190-233
44
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3vyka_ (A:)
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(
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
C-type lectin-like
(322)
Superfamily
:
C-type lectin-like
(322)
Family
:
automated matches
(88)
Protein domain
:
automated matches
(88)
Mouse (Mus musculus) [TaxId: 10090]
(14)
1a
d3vyka_
A:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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