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2Z66
Biol. Unit 3
Info
Asym.Unit (226 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (58 KB)
Biol.Unit 3 (58 KB)
Biol.Unit 4 (58 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE VT3 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61
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
:
1.90
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, Leucine-Rich Repeat, Glycoprotein, Immune Response, Inflammatory Response, Innate Immunity, Membrane, Transmembrane, 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
[
close entry info
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
1h: BETA-D-MANNOSE (BMAh)
2a: BETA-L-FUCOSE (FULa)
2b: BETA-L-FUCOSE (FULb)
2c: BETA-L-FUCOSE (FULc)
2d: BETA-L-FUCOSE (FULd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
3ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
3ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
3ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
3ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
3af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
3z: N-ACETYL-D-GLUCOSAMINE (NAGz)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
FUL
1
Ligand/Ion
BETA-L-FUCOSE
3
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: CC5 (SOFTWARE)
02: CC6 (SOFTWARE)
03: CC7 (SOFTWARE)
04: CC8 (SOFTWARE)
05: CC9 (SOFTWARE)
06: DC1 (SOFTWARE)
07: DC2 (SOFTWARE)
08: DC3 (SOFTWARE)
09: DC4 (SOFTWARE)
10: DC5 (SOFTWARE)
11: DC6 (SOFTWARE)
12: FC2 (SOFTWARE)
13: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC5
SOFTWARE
ASP C:550 , SER C:552 , ASN C:575 , VAL C:602 , NAG C:1421 , NAG C:1432 , HOH C:2294
BINDING SITE FOR RESIDUE NAG C 1431
02
CC6
SOFTWARE
VAL C:548 , PHE C:573 , NAG C:1421 , NAG C:1431 , BMA C:1433
BINDING SITE FOR RESIDUE NAG C 1432
03
CC7
SOFTWARE
NAG C:1432
BINDING SITE FOR RESIDUE BMA C 1433
04
CC8
SOFTWARE
SER C:504 , GLN C:505 , ASN C:526 , ASP C:550 , NAG C:1422 , NAG C:1431 , NAG C:1432 , HOH C:2125 , HOH C:2441
BINDING SITE FOR RESIDUE NAG C 1421
05
CC9
SOFTWARE
LEU C:553 , NAG C:1421 , HOH C:2441
BINDING SITE FOR RESIDUE NAG C 1422
06
DC1
SOFTWARE
ASN C:624 , FUL C:1402 , NAG C:1403
BINDING SITE FOR RESIDUE NAG C 1401
07
DC2
SOFTWARE
NAG C:1401 , NAG C:1403
BINDING SITE FOR RESIDUE FUL C 1402
08
DC3
SOFTWARE
NAG C:1401 , FUL C:1402 , BMA C:1404
BINDING SITE FOR RESIDUE NAG C 1403
09
DC4
SOFTWARE
NAG C:1403
BINDING SITE FOR RESIDUE BMA C 1404
10
DC5
SOFTWARE
SER C:472 , ASN C:497 , NAG C:1412
BINDING SITE FOR RESIDUE NAG C 1411
11
DC6
SOFTWARE
NAG C:1411
BINDING SITE FOR RESIDUE NAG C 1412
12
FC2
SOFTWARE
THR C:558 , GLU C:586 , HIS C:587 , SER C:589 , PHE C:590 , HOH C:2042 , HOH C:2110 , HOH C:2146 , SER D:26 , ARG D:27
BINDING SITE FOR RESIDUE SO4 C 2003
13
FC3
SOFTWARE
SER C:26 , ARG C:27 , HOH C:2159 , THR D:558 , GLU D:586 , HIS D:587 , SER D:589 , PHE D:590 , HOH D:2036 , HOH D:2119
BINDING SITE FOR RESIDUE SO4 D 2004
[
close Site info
]
SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_021977 (T54A, chain C, )
2: VAR_018729 (Q64R, chain C, )
3: VAR_037668 (L385F, chain C, )
4: VAR_012740 (T399I, chain C, )
5: VAR_020335 (S400N, chain C, )
6: VAR_018732 (F443L, chain C, )
7: VAR_018733 (E474K, chain C, )
8: VAR_018734 (Q510H, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021977
T
175
A
TLR4_HUMAN
Polymorphism
16906079
C
T
54
A
2
UniProt
VAR_018729
Q
188
R
TLR4_HUMAN
Polymorphism
5030713
C
Q
64
R
3
UniProt
VAR_037668
L
385
F
TLR4_HUMAN
Polymorphism
11536884
C
L
385
F
4
UniProt
VAR_012740
T
399
I
TLR4_HUMAN
Polymorphism
4986791
C
T
399
I
5
UniProt
VAR_020335
S
400
N
TLR4_HUMAN
Polymorphism
4987233
C
S
400
N
6
UniProt
VAR_018732
F
443
L
TLR4_HUMAN
Polymorphism
5030716
C
F
443
L
7
UniProt
VAR_018733
E
474
K
TLR4_HUMAN
Polymorphism
5030718
C
E
474
K
8
UniProt
VAR_018734
Q
510
H
TLR4_HUMAN
Polymorphism
5030719
C
Q
510
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 10)
Info
All PROSITE Patterns/Profiles
1: LRR (C:26-28,C:32-41,C:56-65,C:51-51,C:...)
;
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
10
-
-
-
C:26-28
-
-
-
C:32-41
-
-
-
C:56-65
-
-
-
C:51-51
-
-
-
C:383-394
-
-
-
C:400-422
-
-
-
C:423-444
-
-
-
C:497-518
-
-
-
C:521-542
-
-
-
C:545-565
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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
(2, 24)
Info
all PFAM domains
1a: PFAM_LRR_6_2z66D01 (D:383-395)
1b: PFAM_LRR_6_2z66D02 (D:383-395)
1c: PFAM_LRR_6_2z66D03 (D:383-395)
1d: PFAM_LRR_6_2z66D04 (D:383-395)
2a: PFAM_LRR_8_2z66D05 (D:496-556)
2b: PFAM_LRR_8_2z66D06 (D:496-556)
2c: PFAM_LRR_8_2z66D07 (D:496-556)
2d: PFAM_LRR_8_2z66D08 (D:496-556)
2e: PFAM_LRR_8_2z66D09 (D:496-556)
2f: PFAM_LRR_8_2z66D10 (D:496-556)
2g: PFAM_LRR_8_2z66D11 (D:496-556)
2h: PFAM_LRR_8_2z66D12 (D:496-556)
2i: PFAM_LRR_8_2z66D13 (D:496-556)
2j: PFAM_LRR_8_2z66D14 (D:496-556)
2k: PFAM_LRR_8_2z66D15 (D:496-556)
2l: PFAM_LRR_8_2z66D16 (D:496-556)
2m: PFAM_LRR_8_2z66D17 (D:496-556)
2n: PFAM_LRR_8_2z66D18 (D:496-556)
2o: PFAM_LRR_8_2z66D19 (D:496-556)
2p: PFAM_LRR_8_2z66D20 (D:496-556)
2q: PFAM_LRR_8_2z66D21 (D:496-556)
2r: PFAM_LRR_8_2z66D22 (D:496-556)
2s: PFAM_LRR_8_2z66D23 (D:496-556)
2t: PFAM_LRR_8_2z66D24 (D:496-556)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LRR
(77)
Family
:
LRR_6
(24)
Homo sapiens (Human)
(4)
1a
LRR_6-2z66D01
D:383-395
1b
LRR_6-2z66D02
D:383-395
1c
LRR_6-2z66D03
D:383-395
1d
LRR_6-2z66D04
D:383-395
Family
:
LRR_8
(41)
Homo sapiens (Human)
(24)
2a
LRR_8-2z66D05
D:496-556
2b
LRR_8-2z66D06
D:496-556
2c
LRR_8-2z66D07
D:496-556
2d
LRR_8-2z66D08
D:496-556
2e
LRR_8-2z66D09
D:496-556
2f
LRR_8-2z66D10
D:496-556
2g
LRR_8-2z66D11
D:496-556
2h
LRR_8-2z66D12
D:496-556
2i
LRR_8-2z66D13
D:496-556
2j
LRR_8-2z66D14
D:496-556
2k
LRR_8-2z66D15
D:496-556
2l
LRR_8-2z66D16
D:496-556
2m
LRR_8-2z66D17
D:496-556
2n
LRR_8-2z66D18
D:496-556
2o
LRR_8-2z66D19
D:496-556
2p
LRR_8-2z66D20
D:496-556
2q
LRR_8-2z66D21
D:496-556
2r
LRR_8-2z66D22
D:496-556
2s
LRR_8-2z66D23
D:496-556
2t
LRR_8-2z66D24
D:496-556
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Asymmetric Unit 1
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Asym.Unit (226 KB)
Header - Asym.Unit
Biol.Unit 1 (58 KB)
Header - Biol.Unit 1
Biol.Unit 2 (58 KB)
Header - Biol.Unit 2
Biol.Unit 3 (58 KB)
Header - Biol.Unit 3
Biol.Unit 4 (58 KB)
Header - Biol.Unit 4
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