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2Z63
Asym. Unit
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Asym.Unit (106 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE TV8 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61
Authors
:
H. M. Kim, B. S. Park, J. -O. Lee
Date
:
22 Jul 07 (Deposition) - 18 Sep 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Tlr4, Toll-Like Receptor, Md-2, Lps, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
(2, 5)
Info
All Hetero Components
1a: BETA-L-FUCOSE (FULa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUL
1
Ligand/Ion
BETA-L-FUCOSE
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:305 , ASN A:309 , FUL A:1402 , NAG A:1403
BINDING SITE FOR RESIDUE NAG A 1401
2
AC2
SOFTWARE
NAG A:1401 , NAG A:1403
BINDING SITE FOR RESIDUE FUL A 1402
3
AC3
SOFTWARE
NAG A:1401 , FUL A:1402
BINDING SITE FOR RESIDUE NAG A 1403
4
AC4
SOFTWARE
SER A:472 , ASN A:497 , GLN A:507 , HOH A:1185 , HOH A:1195 , NAG A:1412
BINDING SITE FOR RESIDUE NAG A 1411
5
AC5
SOFTWARE
ARG A:460 , GLN A:507 , HOH A:1040 , HOH A:1196 , HOH A:1197 , NAG A:1411
BINDING SITE FOR RESIDUE NAG A 1412
[
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SAPs(SNPs)/Variants
(14, 14)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_021977 (T175A, chain A, )
02: VAR_018729 (Q188R, chain A, )
03: VAR_018730 (C246S, chain A, )
04: VAR_012739 (D299G, chain A, )
05: VAR_047563 (C306W, chain A, )
06: VAR_047564 (V310G, chain A, )
07: VAR_018731 (N329S, chain A, )
08: VAR_020334 (F342Y, chain A, )
09: VAR_037668 (L385F, chain A, )
10: VAR_012740 (T399I, chain A, )
11: VAR_020335 (S400N, chain A, )
12: VAR_018732 (F443L, chain A, )
13: VAR_018733 (E474K, chain A, )
14: VAR_018734 (Q510H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_021977
T
175
A
TLR4_HUMAN
Polymorphism
16906079
A
T
175
A
02
UniProt
VAR_018729
Q
188
R
TLR4_HUMAN
Polymorphism
5030713
A
Q
188
R
03
UniProt
VAR_018730
C
246
S
TLR4_HUMAN
Polymorphism
5030714
A
C
246
S
04
UniProt
VAR_012739
D
299
G
TLR4_HUMAN
Polymorphism
4986790
A
D
299
G
05
UniProt
VAR_047563
C
306
W
TLR4_HUMAN
Polymorphism
2770145
A
C
306
W
06
UniProt
VAR_047564
V
310
G
TLR4_HUMAN
Polymorphism
2770144
A
V
310
G
07
UniProt
VAR_018731
N
329
S
TLR4_HUMAN
Polymorphism
5030715
A
N
329
S
08
UniProt
VAR_020334
F
342
Y
TLR4_HUMAN
Polymorphism
5031050
A
F
342
Y
09
UniProt
VAR_037668
L
385
F
TLR4_HUMAN
Polymorphism
11536884
A
L
385
F
10
UniProt
VAR_012740
T
399
I
TLR4_HUMAN
Polymorphism
4986791
A
T
399
I
11
UniProt
VAR_020335
S
400
N
TLR4_HUMAN
Polymorphism
4987233
A
S
400
N
12
UniProt
VAR_018732
F
443
L
TLR4_HUMAN
Polymorphism
5030716
A
F
443
L
13
UniProt
VAR_018733
E
474
K
TLR4_HUMAN
Polymorphism
5030718
A
E
474
K
14
UniProt
VAR_018734
Q
510
H
TLR4_HUMAN
Polymorphism
5030719
A
Q
510
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 11)
Info
All PROSITE Patterns/Profiles
1: LRR (A:55-76|A:79-100|A:103-124|A:176-1...)
;
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
11
A:55-76
A:79-100
A:103-124
A:176-199
A:151-172
A:374-394
A:400-422
A:423-444
A:497-518
A:521-536
A:543-543
[
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]
Exons
(3, 3)
Info
All Exons
Exon 1.1b (A:27-31)
Exon 1.3a (A:32-87)
Exon 1.4c (A:87-596 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.3a
3: Boundary 1.3a/1.4c
4: Boundary 1.4c/-
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
1.1b
ENST00000355622
1b
ENSE00001946124
chr9:
120466650-120466843
194
TLR4_HUMAN
1-31
31
1
A:27-31
5
1.3a
ENST00000355622
3a
ENSE00001654637
chr9:
120470841-120471007
167
TLR4_HUMAN
32-87
56
1
A:32-87
56
1.4c
ENST00000355622
4c
ENSE00001462052
chr9:
120474667-120479149
4483
TLR4_HUMAN
87-839
753
1
A:87-596 (gaps)
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, 9)
Info
all PFAM domains
1a: PFAM_LRR_4_2z63A01 (A:150-199)
2a: PFAM_LRR_6_2z63A02 (A:372-395)
3a: PFAM_LRR_8_2z63A03 (A:496-527)
3b: PFAM_LRR_8_2z63A04 (A:496-527)
3c: PFAM_LRR_8_2z63A05 (A:496-527)
3d: PFAM_LRR_8_2z63A06 (A:496-527)
3e: PFAM_LRR_8_2z63A07 (A:496-527)
3f: PFAM_LRR_8_2z63A08 (A:496-527)
3g: PFAM_LRR_8_2z63A09 (A:496-527)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LRR
(77)
Family
:
LRR_4
(28)
Homo sapiens (Human)
(6)
1a
LRR_4-2z63A01
A:150-199
Family
:
LRR_6
(24)
Homo sapiens (Human)
(4)
2a
LRR_6-2z63A02
A:372-395
Family
:
LRR_8
(41)
Homo sapiens (Human)
(24)
3a
LRR_8-2z63A03
A:496-527
3b
LRR_8-2z63A04
A:496-527
3c
LRR_8-2z63A05
A:496-527
3d
LRR_8-2z63A06
A:496-527
3e
LRR_8-2z63A07
A:496-527
3f
LRR_8-2z63A08
A:496-527
3g
LRR_8-2z63A09
A:496-527
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Asymmetric Unit 1
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