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2Z64
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (128 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MOUSE TLR4 AND MOUSE MD-2 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
:
2.84
Chains
:
Asym. Unit : A,C
Biol. Unit 1: A,C (1x)
Keywords
:
Tlr4, Toll-Like Receptor, Md-2, Lps, Disease Mutation, Glycoprotein, Immune Response, Inflammatory Response, Innate Immunity, Leucine- Rich Repeat, Membrane, Transmembrane, Secreted, 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
]
Hetero Components
(4, 21)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: BETA-L-FUCOSE (FULa)
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)
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)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
4c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
4d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
4e: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGe)
4f: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
FUL
1
Ligand/Ion
BETA-L-FUCOSE
3
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
6
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(21, 21)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:548 , SER A:550 , ASN A:572 , VAL A:599 , NAG A:1412 , NAG A:1421 , NAG A:1422
BINDING SITE FOR RESIDUE NAG A 1411
02
AC2
SOFTWARE
THR A:546 , NAG A:1411 , NAG A:1421
BINDING SITE FOR RESIDUE NAG A 1412
03
AC3
SOFTWARE
SER A:502 , LEU A:522 , ASN A:524 , SER A:526 , ASP A:548 , NAG A:1411 , NAG A:1412 , NAG A:1422
BINDING SITE FOR RESIDUE NAG A 1421
04
AC4
SOFTWARE
NAG A:1411 , NAG A:1421 , BMA A:1423
BINDING SITE FOR RESIDUE NAG A 1422
05
AC5
SOFTWARE
NAG A:1422 , HOH A:1615
BINDING SITE FOR RESIDUE BMA A 1423
06
AC6
SOFTWARE
ASN A:34 , HOH A:1577
BINDING SITE FOR RESIDUE NAG A 1431
07
AC7
SOFTWARE
ASN A:75 , HOH A:1609
BINDING SITE FOR RESIDUE NDG A 1441
08
AC8
SOFTWARE
GLY A:146 , ASN A:172
BINDING SITE FOR RESIDUE NDG A 1451
09
AC9
SOFTWARE
ASN A:204 , HIS A:228 , NAG A:1463
BINDING SITE FOR RESIDUE NAG A 1461
10
BC1
SOFTWARE
HIS A:228 , ARG A:256 , NAG A:1461 , BMA A:1464
BINDING SITE FOR RESIDUE NAG A 1463
11
BC2
SOFTWARE
NAG A:1463 , HOH A:1614
BINDING SITE FOR RESIDUE BMA A 1464
12
BC3
SOFTWARE
ASN A:237
BINDING SITE FOR RESIDUE NDG A 1471
13
BC4
SOFTWARE
ASN A:307 , HIS A:327 , HOH A:1535 , HOH A:1588 , HOH A:1601
BINDING SITE FOR RESIDUE NDG A 1481
14
BC5
SOFTWARE
LEU A:466 , ASN A:492 , HOH A:1556
BINDING SITE FOR RESIDUE NAG A 1491
15
BC6
SOFTWARE
ASN C:26 , HOH C:1530 , HOH C:1550
BINDING SITE FOR RESIDUE NAG C 1501
16
BC7
SOFTWARE
GLU C:64 , ASN C:114 , HOH C:1539
BINDING SITE FOR RESIDUE NDG C 1511
17
BC8
SOFTWARE
GLN C:22 , ASP C:38 , ARG C:132 , ASN C:150 , THR C:152
BINDING SITE FOR RESIDUE NDG C 1521
18
BC9
SOFTWARE
GLN A:589 , ASN A:621 , FUL A:1532 , NAG A:1533
BINDING SITE FOR RESIDUE NAG A 1531
19
CC1
SOFTWARE
NAG A:1531 , NAG A:1533
BINDING SITE FOR RESIDUE FUL A 1532
20
CC2
SOFTWARE
GLN A:589 , GLU A:593 , NAG A:1531 , FUL A:1532 , BMA A:1534
BINDING SITE FOR RESIDUE NAG A 1533
21
CC3
SOFTWARE
NAG A:1533
BINDING SITE FOR RESIDUE BMA A 1534
[
close Site info
]
SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_TLR4_MOUSE_001 (D94N, chain A, )
02: VAR_TLR4_MOUSE_002 (M209I, chain A, )
03: VAR_TLR4_MOUSE_003 (D219G, chain A, )
04: VAR_TLR4_MOUSE_004 (V254I, chain A, )
05: VAR_TLR4_MOUSE_005 (Q423L, chain A, )
06: VAR_TLR4_MOUSE_006 (A477S, chain A, )
07: VAR_TLR4_MOUSE_007 (T516A, chain A, )
08: VAR_TLR4_MOUSE_008 (E593D, chain A, )
09: VAR_TLR4_MOUSE_009 (N600I, chain A, )
10: VAR_TLR4_MOUSE_010 (A607V, chain A, )
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
D
94
N
02
UniProt
VAR_TLR4_MOUSE_002
*
M
209
I
TLR4_MOUSE
---
---
A
M
209
I
03
UniProt
VAR_TLR4_MOUSE_003
*
D
219
G
TLR4_MOUSE
---
---
A
D
219
G
04
UniProt
VAR_TLR4_MOUSE_004
*
V
254
I
TLR4_MOUSE
---
---
A
V
254
I
05
UniProt
VAR_TLR4_MOUSE_005
*
Q
423
L
TLR4_MOUSE
---
---
A
Q
423
L
06
UniProt
VAR_TLR4_MOUSE_006
*
A
477
S
TLR4_MOUSE
---
---
A
A
477
S
07
UniProt
VAR_TLR4_MOUSE_007
*
T
516
A
TLR4_MOUSE
---
---
A
T
516
A
08
UniProt
VAR_TLR4_MOUSE_008
*
E
593
D
TLR4_MOUSE
---
---
A
E
593
D
09
UniProt
VAR_TLR4_MOUSE_009
*
N
600
I
TLR4_MOUSE
---
---
A
N
600
I
10
UniProt
VAR_TLR4_MOUSE_010
*
A
607
V
TLR4_MOUSE
---
---
A
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:
Select:
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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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
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
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)
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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