PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2Z65
Biol. Unit 1
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)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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:
[
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
(3, 5)
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
-1
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
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:148 , LYS A:150 , ASN A:173 , HOH A:1429 , HOH A:1439
BINDING SITE FOR RESIDUE NAG A 1401
2
AC2
SOFTWARE
LEU A:203 , ASN A:205 , ARG A:227 , NAG A:1303 , HOH A:1443
BINDING SITE FOR RESIDUE NAG A 1301
3
AC3
SOFTWARE
NAG A:1301 , BMA A:1304
BINDING SITE FOR RESIDUE NAG A 1303
4
AC4
SOFTWARE
NAG A:1303 , HOH A:1445 , ASN C:49
BINDING SITE FOR RESIDUE BMA A 1304
5
AC5
SOFTWARE
ASN A:35
BINDING SITE FOR RESIDUE NDG A 1201
6
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
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_021977 (T175A, chain A, )
2: VAR_018729 (Q188R, chain A, )
3: VAR_018733 (Q253K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
3
UniProt
VAR_021977
T
175
A
TLR4_HUMAN
Polymorphism
16906079
A
T
175
A
4
UniProt
VAR_018729
Q
188
R
TLR4_HUMAN
Polymorphism
5030713
A
Q
188
R
5
UniProt
VAR_018733
E
474
K
TLR4_HUMAN
Polymorphism
5030718
A
Q
253
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 7)
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
7
A:55-76
-
A:79-100
-
A:103-124
-
A:176-199
-
A:151-172
-
-
-
-
-
A:261-264
-
A:265-281
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
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:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
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
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
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") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (155 KB)
Header - Asym.Unit
Biol.Unit 1 (50 KB)
Header - Biol.Unit 1
Biol.Unit 2 (50 KB)
Header - Biol.Unit 2
Biol.Unit 3 (29 KB)
Header - Biol.Unit 3
Biol.Unit 4 (30 KB)
Header - Biol.Unit 4
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2Z65
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help