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2A0Z
Asym. Unit
Info
Asym.Unit (135 KB)
Biol.Unit 1 (126 KB)
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(1)
Title
:
THE MOLECULAR STRUCTURE OF TOLL-LIKE RECEPTOR 3 LIGAND BINDING DOMAIN
Authors
:
J. K. Bell, I. Botos, P. R. Hall, J. Askins, J. Shiloach, D. M. Segal, D. R.
Date
:
17 Jun 05 (Deposition) - 02 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Leucine Rich Repeat, Solenoid, Glycosylation, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. K. Bell, I. Botos, P. R. Hall, J. Askins, J. Shiloach, D. M. Segal, D. R. Davies
The Molecular Structure Of The Toll-Like Receptor 3 Ligand-Binding Domain
Proc. Natl. Acad. Sci. Usa V. 102 10976 2005
[
close entry info
]
Hetero Components
(8, 33)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: BETA-MERCAPTOETHANOL (BMEa)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: ALPHA-D-GLUCOSE (GLCa)
4b: ALPHA-D-GLUCOSE (GLCb)
5a: ALPHA-D-MANNOSE (MANa)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6m: N-ACETYL-D-GLUCOSAMINE (NAGm)
6n: N-ACETYL-D-GLUCOSAMINE (NAGn)
6o: N-ACETYL-D-GLUCOSAMINE (NAGo)
6p: N-ACETYL-D-GLUCOSAMINE (NAGp)
6q: N-ACETYL-D-GLUCOSAMINE (NAGq)
6r: N-ACETYL-D-GLUCOSAMINE (NAGr)
6s: N-ACETYL-D-GLUCOSAMINE (NAGs)
6t: N-ACETYL-D-GLUCOSAMINE (NAGt)
7a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
8a: SULFATE ION (SO4a)
8b: SULFATE ION (SO4b)
8c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
BME
1
Ligand/Ion
BETA-MERCAPTOETHANOL
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
GLC
2
Ligand/Ion
ALPHA-D-GLUCOSE
5
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
20
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
8
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(33, 33)
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: AC9 (SOFTWARE)
09: AD1 (SOFTWARE)
10: AD2 (SOFTWARE)
11: AD3 (SOFTWARE)
12: AD4 (SOFTWARE)
13: AD5 (SOFTWARE)
14: BC1 (SOFTWARE)
15: BC2 (SOFTWARE)
16: BC5 (SOFTWARE)
17: BC6 (SOFTWARE)
18: BC8 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:33 , ASN A:52 , NAG A:728 , HOH A:6652
BINDING SITE FOR RESIDUE NAG A 727
02
AC2
SOFTWARE
NAG A:727
BINDING SITE FOR RESIDUE NAG A 728
03
AC3
SOFTWARE
THR A:43 , GLN A:44 , VAL A:45 , ASN A:70 , NAG A:730
BINDING SITE FOR RESIDUE NAG A 729
04
AC4
SOFTWARE
GLN A:44 , NAG A:729
BINDING SITE FOR RESIDUE NAG A 730
05
AC5
SOFTWARE
GLU A:171 , ASN A:196
BINDING SITE FOR RESIDUE NAG A 1961
06
AC6
SOFTWARE
ARG A:251 , ASN A:252 , TYR A:302 , NAG A:2522 , HOH A:6717
BINDING SITE FOR RESIDUE NAG A 2521
07
AC7
SOFTWARE
NAG A:2521 , HOH A:6717
BINDING SITE FOR RESIDUE NAG A 2522
08
AC9
SOFTWARE
ASN A:265 , TRP A:296 , NAG A:2652
BINDING SITE FOR RESIDUE NAG A 2651
09
AD1
SOFTWARE
NAG A:2651 , BMA A:2653
BINDING SITE FOR RESIDUE NAG A 2652
10
AD2
SOFTWARE
NAG A:2751
BINDING SITE FOR RESIDUE NAG A 2752
11
AD3
SOFTWARE
ASN A:291 , SER A:315 , HIS A:316 , NAG A:2912 , HOH A:6434
BINDING SITE FOR RESIDUE NAG A 2911
12
AD4
SOFTWARE
SO4 A:752 , NAG A:3981 , FUC A:3986
BINDING SITE FOR RESIDUE NAG A 3982
13
AD5
SOFTWARE
GLU A:363 , SER A:387 , ASN A:413 , ASP A:437 , TYR A:462 , GLC A:753 , NAG A:4132
BINDING SITE FOR RESIDUE NAG A 4131
14
BC1
SOFTWARE
NAG A:2652
BINDING SITE FOR RESIDUE BMA A 2653
15
BC2
SOFTWARE
TRP A:273 , ASN A:275 , NAG A:2752 , HOH A:6580
BINDING SITE FOR RESIDUE NAG A 2751
16
BC5
SOFTWARE
NAG A:2911
BINDING SITE FOR RESIDUE NAG A 2912
17
BC6
SOFTWARE
ASN A:398 , GLU A:399 , SO4 A:752 , NAG A:3982 , FUC A:3986
BINDING SITE FOR RESIDUE NAG A 3981
18
BC8
SOFTWARE
NAG A:3981 , NAG A:3982
BINDING SITE FOR RESIDUE FUC A 3986
19
CC1
SOFTWARE
LYS A:416 , GLC A:753 , NAG A:4131 , BMA A:4133
BINDING SITE FOR RESIDUE NAG A 4132
20
CC2
SOFTWARE
NAG A:4132 , MAN A:4134 , BMA A:4135
BINDING SITE FOR RESIDUE BMA A 4133
21
CC3
SOFTWARE
BMA A:4133
BINDING SITE FOR RESIDUE MAN A 4134
22
CC4
SOFTWARE
BMA A:4133
BINDING SITE FOR RESIDUE BMA A 4135
23
CC5
SOFTWARE
SER A:481 , ASN A:507 , LYS A:531 , NAG A:5072 , FUC A:5076 , HOH A:6523 , HOH A:6690
BINDING SITE FOR RESIDUE NAG A 5071
24
CC6
SOFTWARE
NAG A:5071 , FUC A:5076
BINDING SITE FOR RESIDUE NAG A 5072
25
CC7
SOFTWARE
NAG A:5071 , NAG A:5072 , HOH A:6523
BINDING SITE FOR RESIDUE FUC A 5076
26
CC8
SOFTWARE
ARG A:635 , ASN A:636 , NDG A:6362
BINDING SITE FOR RESIDUE NAG A 6361
27
CC9
SOFTWARE
NAG A:6361
BINDING SITE FOR RESIDUE NDG A 6362
28
DC1
SOFTWARE
ASP A:437 , GLY A:439 , TYR A:462 , NAG A:4131 , NAG A:4132
BINDING SITE FOR RESIDUE GLC A 753
29
DC2
SOFTWARE
TYR A:556 , LYS A:559 , GLU A:580 , HOH A:6713
BINDING SITE FOR RESIDUE GLC A 754
30
DC3
SOFTWARE
NAG A:3981 , NAG A:3982 , HOH A:6646
BINDING SITE FOR RESIDUE SO4 A 752
31
DC4
SOFTWARE
TYR A:326 , ASN A:328 , HIS A:359 , ASN A:361 , HOH A:6392
BINDING SITE FOR RESIDUE SO4 A 750
32
DC5
SOFTWARE
ARG A:488 , ASN A:515 , GLN A:538 , HIS A:539 , HOH A:6414 , HOH A:6693 , HOH A:6695
BINDING SITE FOR RESIDUE SO4 A 751
33
DC6
SOFTWARE
CYS A:356
BINDING SITE FOR RESIDUE BME A 1270
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_052361 (N284I, chain A, )
2: VAR_052362 (Y307D, chain A, )
3: VAR_021976 (L412F, chain A, )
4: VAR_054887 (P554S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_052361
N
284
I
TLR3_HUMAN
Polymorphism
5743316
A
N
284
I
2
UniProt
VAR_052362
Y
307
D
TLR3_HUMAN
Polymorphism
5743317
A
Y
307
D
3
UniProt
VAR_021976
L
412
F
TLR3_HUMAN
Polymorphism
3775291
A
L
412
F
4
UniProt
VAR_054887
P
554
S
TLR3_HUMAN
Disease (HSE2)
---
A
P
554
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 19)
Info
All PROSITE Patterns/Profiles
1: LRR (A:52-73|A:76-97|A:100-121|A:124-14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LRR
PS51450
Leucine-rich repeat profile.
TLR3_HUMAN
52-73
76-97
100-121
124-145
148-168
172-193
198-219
249-270
275-296
299-320
356-377
380-400
408-429
432-454
507-528
531-552
563-584
587-608
611-632
19
A:52-73
A:76-97
A:100-121
A:124-145
A:148-168
A:172-193
A:198-219
A:249-270
A:275-296
A:299-320
A:356-377
A:380-400
A:408-429
A:432-454
A:507-528
A:531-552
A:563-584
A:587-608
A:611-632
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.2 (A:26-147)
Exon 1.3 (A:148-211)
Exon 1.4f (A:212-696)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4f
4: Boundary 1.4f/1.5c
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
ENST00000296795
1a
ENSE00002039207
chr4:
186990306-186990402
97
TLR3_HUMAN
-
0
0
-
-
1.2
ENST00000296795
2
ENSE00001083670
chr4:
186997767-186998214
448
TLR3_HUMAN
1-147
147
1
A:26-147
122
1.3
ENST00000296795
3
ENSE00001083669
chr4:
186999994-187000185
192
TLR3_HUMAN
148-211
64
1
A:148-211
64
1.4f
ENST00000296795
4f
ENSE00001083667
chr4:
187003474-187005326
1853
TLR3_HUMAN
212-829
618
1
A:212-696
485
1.5c
ENST00000296795
5c
ENSE00001375046
chr4:
187005799-187006255
457
TLR3_HUMAN
829-904
76
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in chain 'A'
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