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1Q8M
Asym. Unit
Info
Asym.Unit (91 KB)
Biol.Unit 1 (45 KB)
Biol.Unit 2 (44 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE HUMAN MYELOID CELL ACTIVATING RECEPTOR TREM-1
Authors
:
S. Radaev, M. Kattah, B. Rostro, M. Colonna, P. D. Sun
Date
:
21 Aug 03 (Deposition) - 09 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
V-Type Ig-Like Domain, Immunoglobulin-Like, Immune System Receptor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Radaev, M. Kattah, B. Rostro, M. Colonna, P. D. Sun
Crystal Structure Of The Human Myeloid Cell Activating Receptor Trem-1
Structure V. 11 1527 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 11)
Info
All Hetero Components
1a: GLUTATHIONE (GSHa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GSH
1
Ligand/Ion
GLUTATHIONE
2
SO4
10
Ligand/Ion
SULFATE ION
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:28 , ARG A:130 , LYS B:120
BINDING SITE FOR RESIDUE SO4 A 400
02
AC2
SOFTWARE
LYS B:120 , HOH B:1406
BINDING SITE FOR RESIDUE SO4 B 500
03
AC3
SOFTWARE
ARG A:84
BINDING SITE FOR RESIDUE SO4 A 600
04
AC4
SOFTWARE
LYS A:23 , LYS B:47
BINDING SITE FOR RESIDUE SO4 A 700
05
AC5
SOFTWARE
LYS A:120 , LYS B:28 , ARG B:130
BINDING SITE FOR RESIDUE SO4 B 1400
06
AC6
SOFTWARE
LYS C:28 , ARG C:130 , HOH C:2625 , LYS D:120
BINDING SITE FOR RESIDUE SO4 C 2400
07
AC7
SOFTWARE
LYS D:120 , HOH D:3705
BINDING SITE FOR RESIDUE SO4 D 2500
08
AC8
SOFTWARE
ARG C:84
BINDING SITE FOR RESIDUE SO4 C 2600
09
AC9
SOFTWARE
LYS C:120 , LYS D:28 , ARG D:130
BINDING SITE FOR RESIDUE SO4 D 3400
10
BC1
SOFTWARE
ARG D:59 , LYS D:65
BINDING SITE FOR RESIDUE SO4 D 3700
11
BC2
SOFTWARE
GLN A:52 , THR A:66 , CYS A:69 , TYR A:116 , ASP B:60
BINDING SITE FOR RESIDUE GSH A 999
[
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SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_019333 (T25S, chain A/B/C/D, )
2: VAR_035525 (R97S, chain A/B/C/D, )
3: VAR_049949 (L135T, chain A/B/C/D, )
View:
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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/B/C/D
T
25
S
2
UniProt
VAR_035525
R
97
S
TREM1_HUMAN
Unclassified
---
A/B/C/D
R
97
S
3
UniProt
VAR_049949
K
135
T
TREM1_HUMAN
Polymorphism
34727391
A/B/C/D
L
135
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(3, 12)
Info
All Exons
Exon 1.1 (A:16-17 | B:16-17 | C:16-17 | D:16...)
Exon 1.2 (A:17-136 | B:17-136 | C:17-136 | D...)
Exon 1.3 (A:136-136 | B:136-136 | C:136-136 ...)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
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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
4
A:16-17
B:16-17
C:16-17
D:16-17
2
2
2
2
1.2
ENST00000244709
2
ENSE00000849881
chr6:
41250489-41250133
357
TREM1_HUMAN
17-136
120
4
A:17-136
B:17-136
C:17-136
D:17-136
120
120
120
120
1.3
ENST00000244709
3
ENSE00000750662
chr6:
41248891-41248699
193
TREM1_HUMAN
136-200
65
4
A:136-136
B:136-136
C:136-136
D:136-136
1
1
1
1
1.4
ENST00000244709
4
ENSE00002148464
chr6:
41243968-41243712
257
TREM1_HUMAN
200-234
35
0
-
-
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1q8ma_ (A:)
1b: SCOP_d1q8mb_ (B:)
1c: SCOP_d1q8mc_ (C:)
1d: SCOP_d1q8md_ (D:)
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Protein Domains
(
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(
)
Organisms
(
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(
)
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
d1q8ma_
A:
1b
d1q8mb_
B:
1c
d1q8mc_
C:
1d
d1q8md_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1q8mA00 (A:16-136)
1b: CATH_1q8mB00 (B:16-136)
1c: CATH_1q8mC00 (C:16-136)
1d: CATH_1q8mD00 (D:16-136)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
1q8mA00
A:16-136
1b
1q8mB00
B:16-136
1c
1q8mC00
C:16-136
1d
1q8mD00
D:16-136
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_V_set_1q8mD01 (D:20-133)
1b: PFAM_V_set_1q8mD02 (D:20-133)
1c: PFAM_V_set_1q8mD03 (D:20-133)
1d: PFAM_V_set_1q8mD04 (D:20-133)
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Clan
:
Ig
(577)
Family
:
V-set
(144)
Homo sapiens (Human)
(61)
1a
V-set-1q8mD01
D:20-133
1b
V-set-1q8mD02
D:20-133
1c
V-set-1q8mD03
D:20-133
1d
V-set-1q8mD04
D:20-133
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Asymmetric Unit 1
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Asym.Unit (91 KB)
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