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2Z65
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (50 KB)
Biol.Unit 2 (50 KB)
Biol.Unit 3 (29 KB)
Biol.Unit 4 (30 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE HUMAN TLR4 TV3 HYBRID-MD-2-ERITORAN COMPLEX
Authors
:
J. -O. Lee, H. M. Kim, B. S. Park
Date
:
22 Jul 07 (Deposition) - 18 Sep 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Tlr4, Toll-Like Receptor, Md-2, Lps, E5564, Eritoran, Glycoprotein, Immune Response, Inflammatory Response, Innate Immunity, Leucine- Rich Repeat, Membrane, Transmembrane, Secreted, Immune System
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
H. M. Kim, B. S. Park, J. -I. Kim, S. E. Kim, J. Lee, S. C. Oh, P. Enkhbayar, N. Matsushima, H. Lee, O. J. Yoo, J. -O. Lee
Crystal Structure Of The Tlr4-Md-2 Complex With Bound Endotoxin Antagonist Eritoran
Cell(Cambridge, Mass. ) V. 130 906 2007
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O... (E55a)
2b: 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O... (E55b)
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)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
E55
2
Ligand/Ion
3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE
3
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:148 , LYS A:150 , ASN A:173 , HOH A:1429 , HOH A:1439
BINDING SITE FOR RESIDUE NAG A 1401
02
AC2
SOFTWARE
LEU A:203 , ASN A:205 , ARG A:227 , NAG A:1303 , HOH A:1443
BINDING SITE FOR RESIDUE NAG A 1301
03
AC3
SOFTWARE
NAG A:1301 , BMA A:1304
BINDING SITE FOR RESIDUE NAG A 1303
04
AC4
SOFTWARE
NAG A:1303 , HOH A:1445 , ASN C:49
BINDING SITE FOR RESIDUE BMA A 1304
05
AC5
SOFTWARE
ASN A:35
BINDING SITE FOR RESIDUE NDG A 1201
06
AC6
SOFTWARE
HIS B:148 , LYS B:150 , ASN B:173 , HOH B:1403 , HOH B:1407 , HOH B:1417
BINDING SITE FOR RESIDUE NAG B 1401
07
AC7
SOFTWARE
LEU B:203 , ASN B:205 , ARG B:227 , HOH B:1414
BINDING SITE FOR RESIDUE NAG B 1301
08
AC8
SOFTWARE
ASN B:35 , HOH B:1411 , HOH B:1436 , HOH B:1449
BINDING SITE FOR RESIDUE NDG B 1201
09
AC9
SOFTWARE
CYS B:264 , LYS B:294 , SER B:298 , ILE B:299 , ILE B:300 , PRO B:302 , ILE C:46 , TYR C:65 , LEU C:87 , TYR C:102 , PHE C:104 , PHE C:119 , SER C:120 , PHE C:121 , GLY C:123 , PHE C:151
BINDING SITE FOR RESIDUE E55 C 1
10
BC1
SOFTWARE
LYS A:294 , SER A:298 , ILE A:299 , ILE A:300 , PRO A:302 , ILE D:46 , ILE D:63 , TYR D:65 , TYR D:102 , PHE D:104 , PHE D:119 , SER D:120 , PHE D:121 , GLY D:123 , PHE D:151 , HOH D:180
BINDING SITE FOR RESIDUE E55 D 1
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SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_050030 (G56G, chain C/D, )
2: VAR_024532 (P157S, chain C/D, )
3: VAR_021977 (T175A, chain A/B, )
4: VAR_018729 (Q188R, chain A/B, )
5: VAR_018733 (Q253K, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_050030
R
56
G
LY96_HUMAN
Polymorphism
6472812
C/D
G
56
G
2
UniProt
VAR_024532
P
157
S
LY96_HUMAN
Polymorphism
11466004
C/D
P
157
S
3
UniProt
VAR_021977
T
175
A
TLR4_HUMAN
Polymorphism
16906079
A/B
T
175
A
4
UniProt
VAR_018729
Q
188
R
TLR4_HUMAN
Polymorphism
5030713
A/B
Q
188
R
5
UniProt
VAR_018733
E
474
K
TLR4_HUMAN
Polymorphism
5030718
A/B
Q
253
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 14)
Info
All PROSITE Patterns/Profiles
1: LRR (A:55-76,B:55-76|A:79-100,B:79-100|...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LRR
PS51450
Leucine-rich repeat profile.
TLR4_HUMAN
55-76
79-100
103-124
176-199
151-172
374-394
400-422
423-444
497-518
521-542
545-565
14
A:55-76
B:55-76
A:79-100
B:79-100
A:103-124
B:103-124
A:176-199
B:176-199
A:151-172
B:151-172
-
-
-
-
A:261-264
B:261-264
A:265-281
B:265-281
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Exons
(8, 16)
Info
All Exons
Exon 1.1a (C:19-38 | D:19-38)
Exon 1.2 (C:38-68 | D:38-68)
Exon 1.3 (C:68-111 | D:68-111)
Exon 1.4 (C:111-128 | D:111-128)
Exon 1.5b (C:129-158 | D:129-158)
Exon 2.1b (A:27-31 | B:27-31)
Exon 2.3a (A:32-87 | B:32-87)
Exon 2.4c (A:87-302 (gaps) | B:87-302 (gaps))
View:
Select:
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All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5b
06: Boundary 1.5b/-
07: Boundary -/2.1b
08: Boundary 2.1b/2.3a
09: Boundary 2.3a/2.4c
10: Boundary 2.4c/-
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
ENST00000284818
1a
ENSE00001244306
chr8:
74903587-74903789
203
LY96_HUMAN
1-38
38
2
C:19-38
D:19-38
20
20
1.2
ENST00000284818
2
ENSE00001016737
chr8:
74917031-74917120
90
LY96_HUMAN
38-68
31
2
C:38-68
D:38-68
31
31
1.3
ENST00000284818
3
ENSE00001016736
chr8:
74922236-74922364
129
LY96_HUMAN
68-111
44
2
C:68-111
D:68-111
44
44
1.4
ENST00000284818
4
ENSE00001016734
chr8:
74939024-74939076
53
LY96_HUMAN
111-128
18
2
C:111-128
D:111-128
18
18
1.5b
ENST00000284818
5b
ENSE00002121776
chr8:
74941191-74941322
132
LY96_HUMAN
129-160
32
2
C:129-158
D:129-158
30
30
2.1b
ENST00000355622
1b
ENSE00001946124
chr9:
120466650-120466843
194
TLR4_HUMAN
1-31
31
2
A:27-31
B:27-31
5
5
2.3a
ENST00000355622
3a
ENSE00001654637
chr9:
120470841-120471007
167
TLR4_HUMAN
32-87
56
2
A:32-87
B:32-87
56
56
2.4c
ENST00000355622
4c
ENSE00001462052
chr9:
120474667-120479149
4483
TLR4_HUMAN
87-839
753
2
A:87-302 (gaps)
B:87-302 (gaps)
542
542
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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:
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Label:
Sorry, no Info available
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Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_LRR_4_2z65B01 (B:150-199)
1b: PFAM_LRR_4_2z65B02 (B:150-199)
2a: PFAM_LRR_8_2z65B03 (B:78-138)
2b: PFAM_LRR_8_2z65B04 (B:78-138)
2c: PFAM_LRR_8_2z65B05 (B:78-138)
2d: PFAM_LRR_8_2z65B06 (B:78-138)
3a: PFAM_E1_DerP2_DerF2_2z65D01 (D:30-155)
3b: PFAM_E1_DerP2_DerF2_2z65D02 (D:30-155)
View:
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Clans
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(
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Families
(
)
(
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Organisms
(
)
(
)
Clan
:
LRR
(77)
Family
:
LRR_4
(28)
Homo sapiens (Human)
(6)
1a
LRR_4-2z65B01
B:150-199
1b
LRR_4-2z65B02
B:150-199
Family
:
LRR_8
(41)
Homo sapiens (Human)
(24)
2a
LRR_8-2z65B03
B:78-138
2b
LRR_8-2z65B04
B:78-138
2c
LRR_8-2z65B05
B:78-138
2d
LRR_8-2z65B06
B:78-138
Clan
:
no clan defined [family: E1_DerP2_DerF2]
(8)
Family
:
E1_DerP2_DerF2
(8)
Homo sapiens (Human)
(1)
3a
E1_DerP2_DerF2-2z65D01
D:30-155
3b
E1_DerP2_DerF2-2z65D02
D:30-155
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Asym.Unit (155 KB)
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