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.
1SMO
Asym. Unit
Info
Asym.Unit (47 KB)
Biol.Unit 1 (42 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 HUMAN TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 1 (TREM-1) AT 1.47 .
Authors
:
M. S. Kelker, T. R. Foss, W. Peti, L. Teyton, J. W. Kelly, I. A. Wilson
Date
:
09 Mar 04 (Deposition) - 21 Sep 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.47
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Activating Receptors, Trem-1, Innate Immune System Receptor, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Kelker, T. R. Foss, W. Peti, L. Teyton, J. W. Kelly, I. A. Wilson
Crystal Structure Of Human Triggering Receptor Expressed On Myeloid Cells 1 (Trem-1) At 1. 47A.
J. Mol. Biol. V. 342 1237 2004
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: L(+)-TARTARIC ACID (TLAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
TLA
1
Ligand/Ion
L(+)-TARTARIC ACID
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:44 , LYS A:47 , HIS A:123 , ASN B:76 , SER B:77 , TYR B:90 , HIS B:91 , ASP B:92 , HIS B:93 , HOH B:728
BINDING SITE FOR RESIDUE TLA B 726
[
close Site info
]
SAPs(SNPs)/Variants
(3, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_019333 (T25S, chain A, )
2: VAR_035525 (R97S, chain A/B, )
3: VAR_049949 (K135T, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_019333
T
25
S
TREM1_HUMAN
Polymorphism
2234237
A
T
25
S
2
UniProt
VAR_035525
R
97
S
TREM1_HUMAN
Unclassified
---
A/B
R
97
S
3
UniProt
VAR_049949
K
135
T
TREM1_HUMAN
Polymorphism
34727391
B
K
135
T
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
[
close PROSITE info
]
Exons
(1, 2)
Info
All Exons
Exon 1.2 (A:21-133 | B:26-135)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
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
1.1
ENST00000244709
1
ENSE00001338886
chr6:
41254457-41254345
113
TREM1_HUMAN
1-17
17
0
-
-
1.2
ENST00000244709
2
ENSE00000849881
chr6:
41250489-41250133
357
TREM1_HUMAN
17-136
120
2
A:21-133
B:26-135
113
110
1.3
ENST00000244709
3
ENSE00000750662
chr6:
41248891-41248699
193
TREM1_HUMAN
136-200
65
0
-
-
1.4
ENST00000244709
4
ENSE00002148464
chr6:
41243968-41243712
257
TREM1_HUMAN
200-234
35
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1smoa_ (A:)
1b: SCOP_d1smob_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
TREM-1 (triggering receptor expressed on myeloid cells 1)
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1smoa_
A:
1b
d1smob_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1smoB00 (B:26-135)
1b: CATH_1smoA00 (A:21-133)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
1smoB00
B:26-135
1b
1smoA00
A:21-133
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_V_set_1smoB01 (B:26-133)
1b: PFAM_V_set_1smoB02 (B:26-133)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
V-set
(144)
Homo sapiens (Human)
(61)
1a
V-set-1smoB01
B:26-133
1b
V-set-1smoB02
B:26-133
[
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
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 (47 KB)
Header - Asym.Unit
Biol.Unit 1 (42 KB)
Header - Biol.Unit 1
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
1SMO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
