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3VQ2
Asym. Unit
Info
Asym.Unit (499 KB)
Biol.Unit 1 (489 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MOUSE TLR4/MD-2/LPS COMPLEX
Authors
:
U. Ohto, T. Shimizu
Date
:
17 Mar 12 (Deposition) - 09 May 12 (Release) - 17 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.48
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Leucine Rich Repeat Md-2 Related Lipid Recognition, Receptor Innate Immunity, Lipid Binding, Glycosylation, Secreted, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Ohto, K. Fukase, K. Miyake, T. Shimizu
Structural Basis Of Species-Specific Endotoxin Sensing By Innate Immune Receptor Tlr4/Md-2
Proc. Natl. Acad. Sci. Usa V. 109 7421 2012
[
close entry info
]
Hetero Components
(5, 15)
Info
All Hetero Components
1a: LAURIC ACID (DAOa)
1b: LAURIC ACID (DAOb)
2a: 2-DEOXY-3-O-[(3R)-3-HYDROXYTETRADE... (LP4a)
2b: 2-DEOXY-3-O-[(3R)-3-HYDROXYTETRADE... (LP4b)
3a: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-... (LP5a)
3b: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-... (LP5b)
4a: MYRISTIC ACID (MYRa)
4b: MYRISTIC ACID (MYRb)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DAO
2
Ligand/Ion
LAURIC ACID
2
LP4
2
Ligand/Ion
2-DEOXY-3-O-[(3R)-3-HYDROXYTETRADECANOYL]-2-{[(3R)-3-HYDROXYTETRADECANOYL]AMINO}-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE
3
LP5
2
Ligand/Ion
(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
4
MYR
2
Ligand/Ion
MYRISTIC ACID
5
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(13, 13)
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:146 , GLN A:147 , TYR A:169 , SER A:171 , ASN A:172 , THR B:469 , SER B:470 , ASN B:495
BINDING SITE FOR RESIDUE NAG A 800
02
AC2
SOFTWARE
ASN A:204 , HIS A:228
BINDING SITE FOR RESIDUE NAG A 801
03
AC3
SOFTWARE
ASP A:548 , SER A:550 , ASN A:572 , NAG A:802 , NAG A:803
BINDING SITE FOR RESIDUE NAG A 804
04
AC4
SOFTWARE
LYS A:263 , ILE C:52 , PHE C:65 , LEU C:74 , LEU C:94 , TYR C:102 , PRO C:118 , PHE C:119 , SER C:120 , LP5 C:301 , DAO C:302 , MYR C:303
BINDING SITE FOR RESIDUE LP4 C 300
05
AC5
SOFTWARE
LYS A:360 , SER B:413 , ARG B:434 , LEU C:87 , ARG C:90 , PHE C:121 , GLU C:122 , ILE C:124 , PHE C:126 , PHE C:151 , LP4 C:300 , DAO C:302
BINDING SITE FOR RESIDUE LP5 C 301
06
AC6
SOFTWARE
ARG C:90 , GLU C:92 , TYR C:131 , LP4 C:300 , LP5 C:301
BINDING SITE FOR RESIDUE DAO C 302
07
AC7
SOFTWARE
ILE C:46 , PHE C:76 , GLU C:92 , PHE C:147 , LEU C:149 , LP4 C:300
BINDING SITE FOR RESIDUE MYR C 303
08
AC8
SOFTWARE
LYS B:263 , ILE D:52 , PHE D:65 , LEU D:74 , LEU D:94 , TYR D:102 , PHE D:104 , PHE D:119 , SER D:120 , LP5 D:301 , DAO D:302 , MYR D:303
BINDING SITE FOR RESIDUE LP4 D 300
09
AC9
SOFTWARE
SER A:413 , VAL D:82 , LEU D:87 , ARG D:90 , PHE D:121 , GLU D:122 , ILE D:124 , PHE D:126 , PHE D:151 , LP4 D:300 , DAO D:302
BINDING SITE FOR RESIDUE LP5 D 301
10
BC1
SOFTWARE
ARG D:90 , PHE D:126 , LP4 D:300 , LP5 D:301
BINDING SITE FOR RESIDUE DAO D 302
11
BC2
SOFTWARE
ILE D:46 , PHE D:76 , GLU D:92 , PHE D:147 , LEU D:149 , LP4 D:300
BINDING SITE FOR RESIDUE MYR D 303
12
BC3
SOFTWARE
SER A:502 , LYS A:503 , ASN A:524 , SER A:526 , HIS A:527 , ASP A:548 , NAG A:804
BINDING SITE FOR LINKED RESIDUES A 802 to 803
13
BC4
SOFTWARE
SER B:502 , LYS B:503 , ASN B:524 , SER B:526 , ASP B:548
BINDING SITE FOR LINKED RESIDUES B 701 to 702
[
close Site info
]
SAPs(SNPs)/Variants
(10, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_TLR4_MOUSE_001 (D94N, chain A/B, )
02: VAR_TLR4_MOUSE_002 (M209I, chain A/B, )
03: VAR_TLR4_MOUSE_003 (D219G, chain A/B, )
04: VAR_TLR4_MOUSE_004 (V254I, chain A/B, )
05: VAR_TLR4_MOUSE_005 (Q423L, chain A/B, )
06: VAR_TLR4_MOUSE_006 (A477S, chain A/B, )
07: VAR_TLR4_MOUSE_007 (T516A, chain A/B, )
08: VAR_TLR4_MOUSE_008 (E593D, chain A/B, )
09: VAR_TLR4_MOUSE_009 (N600I, chain A/B, )
10: VAR_TLR4_MOUSE_010 (A607V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_TLR4_MOUSE_001
*
D
94
N
TLR4_MOUSE
---
---
A/B
D
94
N
02
UniProt
VAR_TLR4_MOUSE_002
*
M
209
I
TLR4_MOUSE
---
---
A/B
M
209
I
03
UniProt
VAR_TLR4_MOUSE_003
*
D
219
G
TLR4_MOUSE
---
---
A/B
D
219
G
04
UniProt
VAR_TLR4_MOUSE_004
*
V
254
I
TLR4_MOUSE
---
---
A/B
V
254
I
05
UniProt
VAR_TLR4_MOUSE_005
*
Q
423
L
TLR4_MOUSE
---
---
A/B
Q
423
L
06
UniProt
VAR_TLR4_MOUSE_006
*
A
477
S
TLR4_MOUSE
---
---
A/B
A
477
S
07
UniProt
VAR_TLR4_MOUSE_007
*
T
516
A
TLR4_MOUSE
---
---
A/B
T
516
A
08
UniProt
VAR_TLR4_MOUSE_008
*
E
593
D
TLR4_MOUSE
---
---
A/B
E
593
D
09
UniProt
VAR_TLR4_MOUSE_009
*
N
600
I
TLR4_MOUSE
---
---
A/B
N
600
I
10
UniProt
VAR_TLR4_MOUSE_010
*
A
607
V
TLR4_MOUSE
---
---
A/B
A
607
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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View:
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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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]
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(currently selected atoms:
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)
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Protein & NOT Site
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