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4G8A
Asym. Unit
Info
Asym.Unit (508 KB)
Biol.Unit 1 (497 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN TLR4 POLYMORPHIC VARIANT D299G AND T399I IN COMPLEX WITH MD-2 AND LPS
Authors
:
U. Ohto, T. Shimizu
Date
:
23 Jul 12 (Deposition) - 17 Oct 12 (Release) - 04 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
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, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Ohto, N. Yamakawa, S. Akashi-Takamura, K. Miyake, T. Shimizu
Structural Analyses Of Human Toll-Like Receptor 4 Polymorphisms D299G And T399I
J. Biol. Chem. V. 287 40611 2012
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Hetero Components
(6, 22)
Info
All Hetero Components
1a: LAURIC ACID (DAOa)
1b: LAURIC ACID (DAOb)
2a: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOa)
2b: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOb)
3a: 2-DEOXY-3-O-[(3R)-3-HYDROXYTETRADE... (LP4a)
3b: 2-DEOXY-3-O-[(3R)-3-HYDROXYTETRADE... (LP4b)
4a: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-... (LP5a)
4b: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-... (LP5b)
5a: MYRISTIC ACID (MYRa)
5b: MYRISTIC ACID (MYRb)
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)
View:
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Label:
No.
Name
Count
Type
Full Name
1
DAO
2
Ligand/Ion
LAURIC ACID
2
KDO
2
Ligand/Ion
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
3
LP4
2
Ligand/Ion
2-DEOXY-3-O-[(3R)-3-HYDROXYTETRADECANOYL]-2-{[(3R)-3-HYDROXYTETRADECANOYL]AMINO}-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE
4
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
5
MYR
2
Ligand/Ion
MYRISTIC ACID
6
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(14, 14)
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)
14: BC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:173
BINDING SITE FOR RESIDUE NAG A 701
02
AC2
SOFTWARE
SER A:504 , GLN A:505 , ASN A:526 , ASP A:550 , NAG A:703 , NAG A:704 , NAG A:705
BINDING SITE FOR RESIDUE NAG A 702
03
AC3
SOFTWARE
NAG A:702 , NAG A:704
BINDING SITE FOR RESIDUE NAG A 703
04
AC4
SOFTWARE
ASP A:550 , SER A:552 , ASN A:575 , VAL A:602 , NAG A:702 , NAG A:703 , NAG A:705
BINDING SITE FOR RESIDUE NAG A 704
05
AC5
SOFTWARE
NAG A:702 , NAG A:704
BINDING SITE FOR RESIDUE NAG A 705
06
AC6
SOFTWARE
LYS B:150 , ASN B:173
BINDING SITE FOR RESIDUE NAG B 701
07
AC7
SOFTWARE
SER B:504 , GLN B:505 , ASN B:526 , ASP B:550 , NAG B:703 , NAG B:704 , NAG B:705
BINDING SITE FOR RESIDUE NAG B 702
08
AC8
SOFTWARE
LEU B:553 , NAG B:702 , NAG B:704 , NAG B:705
BINDING SITE FOR RESIDUE NAG B 703
09
AC9
SOFTWARE
SER B:528 , ASP B:550 , SER B:552 , ASN B:575 , VAL B:602 , NAG B:702 , NAG B:703 , NAG B:705
BINDING SITE FOR RESIDUE NAG B 704
10
BC1
SOFTWARE
VAL B:548 , NAG B:702 , NAG B:703 , NAG B:704
BINDING SITE FOR RESIDUE NAG B 705
11
BC2
SOFTWARE
PHE C:64 , ASN C:114
BINDING SITE FOR RESIDUE NAG C 201
12
BC3
SOFTWARE
ASN D:114
BINDING SITE FOR RESIDUE NAG D 201
13
BC4
SOFTWARE
ARG A:264 , TYR A:296 , LYS A:341 , SER B:415 , GLN B:436 , GLU B:439 , PHE B:440 , ILE C:63 , TYR C:65 , PHE C:76 , LEU C:78 , VAL C:82 , LEU C:87 , ARG C:90 , TYR C:102 , ILE C:117 , SER C:118 , PHE C:119 , SER C:120 , PHE C:121 , LYS C:122 , ILE C:124 , PHE C:126 , TYR C:131 , PHE C:151
BINDING SITE FOR LINKED RESIDUES C 202 TO 206
14
BC5
SOFTWARE
SER A:415 , GLN A:436 , GLU A:439 , ARG B:264 , TYR B:296 , ILE D:63 , PHE D:76 , VAL D:82 , LEU D:87 , ARG D:90 , TYR D:102 , PHE D:104 , SER D:118 , PHE D:119 , SER D:120 , PHE D:121 , LYS D:122 , ILE D:124 , PHE D:126 , TYR D:131 , PHE D:151
BINDING SITE FOR LINKED RESIDUES D 202 TO 206
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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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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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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