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.
PLEASE WAIT...
Getting 'Exon' information from database.
3ULA
Asym. Unit
Info
Asym.Unit (145 KB)
Biol.Unit 1 (71 KB)
Biol.Unit 2 (71 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 TV3 MUTANT F63W-MD-2-ERITORAN COMPLEX
Authors
:
H. J. Kim, H. K. Cheong, Y. H. Jeon
Date
:
10 Nov 11 (Deposition) - 04 Apr 12 (Release) - 09 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Lrr, Lps Binding, Md-2, Extracellular Matrix, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Han, H. J. Kim, S. C. Lee, S. Hong, K. Park, Y. H. Jeon, D. Kim, H. K. Cheong, H. S. Kim
Structure-Based Rational Design Of A Toll-Like Receptor 4 (Tlr4) Decoy Receptor With High Binding Affinity For A Target Protein.
Plos One V. 7 30929 2012
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
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)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
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
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:35
BINDING SITE FOR RESIDUE NAG A 1201
02
AC2
SOFTWARE
LEU A:203 , ASN A:205 , ARG A:227 , NAG A:1203
BINDING SITE FOR RESIDUE NAG A 1202
03
AC3
SOFTWARE
NAG A:1202 , BMA A:1204
BINDING SITE FOR RESIDUE NAG A 1203
04
AC4
SOFTWARE
NAG A:1203 , LYS B:128
BINDING SITE FOR RESIDUE BMA A 1204
05
AC5
SOFTWARE
HIS A:148 , LYS A:150 , ASN A:173
BINDING SITE FOR RESIDUE NAG A 1205
06
AC6
SOFTWARE
CYS A:264 , LYS A:294 , SER A:298 , ILE A:299 , ILE A:300 , PRO A:302 , ILE D:46 , PHE D:76 , LEU D:87 , TYR D:102 , SER D:118 , PHE D:119 , SER D:120 , PHE D:121 , GLY D:123 , PHE D:151
BINDING SITE FOR RESIDUE E55 A 1206
07
AC7
SOFTWARE
ILE B:46 , ILE B:52 , ILE B:63 , PHE B:76 , LEU B:87 , SER B:118 , PHE B:119 , SER B:120 , PHE B:121 , GLY B:123 , PHE B:151 , LYS C:294 , SER C:298 , ILE C:299 , ILE C:300 , PRO C:302
BINDING SITE FOR RESIDUE E55 C 401
08
AC8
SOFTWARE
ASN C:35
BINDING SITE FOR RESIDUE NAG C 402
09
AC9
SOFTWARE
LEU C:203 , ASN C:205 , ARG C:227 , NAG C:404
BINDING SITE FOR RESIDUE NAG C 403
10
BC1
SOFTWARE
NAG C:403 , BMA C:405
BINDING SITE FOR RESIDUE NAG C 404
11
BC2
SOFTWARE
NAG C:404
BINDING SITE FOR RESIDUE BMA C 405
12
BC3
SOFTWARE
HIS C:148 , LYS C:150 , ASN C:173
BINDING SITE FOR RESIDUE NAG C 406
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_050030 (G56G, chain B/D, )
2: VAR_024532 (P157S, chain B/D, )
3: VAR_021977 (T175A, chain A/C, )
4: VAR_018729 (Q188R, chain A/C, )
5: VAR_018733 (Q253K, chain A/C, )
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
B/D
G
56
G
2
UniProt
VAR_024532
P
157
S
LY96_HUMAN
Polymorphism
11466004
B/D
P
157
S
3
UniProt
VAR_021977
T
175
A
TLR4_HUMAN
Polymorphism
16906079
A/C
T
175
A
4
UniProt
VAR_018729
Q
188
R
TLR4_HUMAN
Polymorphism
5030713
A/C
Q
188
R
5
UniProt
VAR_018733
E
474
K
TLR4_HUMAN
Polymorphism
5030718
A/C
Q
253
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 14)
Info
All PROSITE Patterns/Profiles
1: LRR (A:55-76,C:55-76|A:79-100,C: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
C:55-76
A:79-100
C:79-100
A:103-124
C:103-124
A:176-199
C:176-199
A:151-172
C:151-172
-
-
-
-
A:261-264
C:261-264
A:265-281
C:265-281
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1a (B:19-38 | D:19-38)
Exon 1.2 (B:38-68 | D:38-68)
Exon 1.3 (B:68-111 | D:68-111)
Exon 1.4 (B:111-128 | D:111-128)
Exon 1.5b (B:129-158 | D:129-158)
Exon 2.1b (A:27-31 | C:27-31)
Exon 2.3a (A:32-87 | C:32-87)
Exon 2.4c (A:87-302 (gaps) | C:87-302 (gaps))
View:
Select:
Label:
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
B:19-38
D:19-38
20
20
1.2
ENST00000284818
2
ENSE00001016737
chr8:
74917031-74917120
90
LY96_HUMAN
38-68
31
2
B:38-68
D:38-68
31
31
1.3
ENST00000284818
3
ENSE00001016736
chr8:
74922236-74922364
129
LY96_HUMAN
68-111
44
2
B:68-111
D:68-111
44
44
1.4
ENST00000284818
4
ENSE00001016734
chr8:
74939024-74939076
53
LY96_HUMAN
111-128
18
2
B:111-128
D:111-128
18
18
1.5b
ENST00000284818
5b
ENSE00002121776
chr8:
74941191-74941322
132
LY96_HUMAN
129-160
32
2
B: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
C:27-31
5
5
2.3a
ENST00000355622
3a
ENSE00001654637
chr9:
120470841-120471007
167
TLR4_HUMAN
32-87
56
2
A:32-87
C:32-87
56
56
2.4c
ENST00000355622
4c
ENSE00001462052
chr9:
120474667-120479149
4483
TLR4_HUMAN
87-839
753
2
A:87-302 (gaps)
C:87-302 (gaps)
542
542
[
close EXON info
]
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
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain B
Chain C
Chain D
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 (145 KB)
Header - Asym.Unit
Biol.Unit 1 (71 KB)
Header - Biol.Unit 1
Biol.Unit 2 (71 KB)
Header - Biol.Unit 2
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
3ULA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help