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Asym. Unit
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Asym.Unit (64 KB)
Biol.Unit 1 (60 KB)
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(1)
Title
:
EXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR RECEPTOR. CRYSTALLIZED AT PH3.7 IN P 21 21 21.
Authors
:
J. H. Naismith, S. R. Sprang
Date
:
03 Jul 96 (Deposition) - 11 Jan 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Binding Protein, Cytokine, Signalling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Naismith, T. Q. Devine, T. Kohno, S. R. Sprang
Structures Of The Extracellular Domain Of The Type I Tumor Necrosis Factor Receptor.
Structure V. 4 1251 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:23 , ARG A:68 , ARG A:99 , HOH A:421
BINDING SITE FOR RESIDUE SO4 A 401
2
AC2
SOFTWARE
ARG A:68 , ARG A:99 , LYS A:100 , HOH A:480 , HOH B:325
BINDING SITE FOR RESIDUE SO4 A 402
3
AC3
SOFTWARE
TYR A:103 , GLN A:133 , ASN A:134 , HOH A:450 , HOH A:466 , HOH A:476
BINDING SITE FOR RESIDUE SO4 A 403
4
AC4
SOFTWARE
GLU A:147 , HOH A:473 , HOH A:497 , HOH B:219 , HOH B:257 , HOH B:275
BINDING SITE FOR RESIDUE MG A 404
[
close Site info
]
SAPs(SNPs)/Variants
(14, 28)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_019329 (H22Q, chain A/B, )
02: VAR_013410 (C30R, chain A/B, )
03: VAR_019302 (C30S, chain A/B, )
04: VAR_019303 (C33G, chain A/B, )
05: VAR_013411 (C33Y, chain A/B, )
06: VAR_019330 (P46L, chain A/B, )
07: VAR_013412 (T50M, chain A/B, )
08: VAR_013413 (C52F, chain A/B, )
09: VAR_019304 (C70S, chain A/B, )
10: VAR_019331 (S86G, chain A/B, )
11: VAR_013414 (C88R, chain A/B, )
12: VAR_013415 (C88Y, chain A/B, )
13: VAR_019305 (R92P, chain A/B, )
14: VAR_019332 (R92Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_019329
H
51
Q
TNR1A_HUMAN
Disease (FHF)
---
A/B
H
22
Q
02
UniProt
VAR_013410
C
59
R
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
30
R
03
UniProt
VAR_019302
C
59
S
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
30
S
04
UniProt
VAR_019303
C
62
G
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
33
G
05
UniProt
VAR_013411
C
62
Y
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
33
Y
06
UniProt
VAR_019330
P
75
L
TNR1A_HUMAN
Disease (FHF)
4149637
A/B
P
46
L
07
UniProt
VAR_013412
T
79
M
TNR1A_HUMAN
Disease (FHF)
---
A/B
T
50
M
08
UniProt
VAR_013413
C
81
F
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
52
F
09
UniProt
VAR_019304
C
99
S
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
70
S
10
UniProt
VAR_019331
S
115
G
TNR1A_HUMAN
Disease (FHF)
---
A/B
S
86
G
11
UniProt
VAR_013414
C
117
R
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
88
R
12
UniProt
VAR_013415
C
117
Y
TNR1A_HUMAN
Disease (FHF)
---
A/B
C
88
Y
13
UniProt
VAR_019305
R
121
P
TNR1A_HUMAN
Disease (FHF)
4149584
A/B
R
92
P
14
UniProt
VAR_019332
R
121
Q
TNR1A_HUMAN
Disease (FHF)
4149584
A/B
R
92
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: TNFR_NGFR_2 (A:14-52,B:14-52|A:54-96,B:54-96|A:...)
2: TNFR_NGFR_1 (A:15-52,B:15-52|A:55-96,B:55-96|A:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNFR_NGFR_2
PS50050
TNFR/NGFR family cysteine-rich region domain profile.
TNR1A_HUMAN
43-81
83-125
126-166
6
A:14-52
B:14-52
A:54-96
B:54-96
A:97-137
B:97-137
2
TNFR_NGFR_1
PS00652
TNFR/NGFR family cysteine-rich region signature.
TNR1A_HUMAN
44-81
84-125
125-166
6
A:15-52
B:15-52
A:55-96
B:55-96
A:96-137
B:96-137
[
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]
Exons
(5, 10)
Info
All Exons
Exon 1.2 (A:13-36 | B:11-36)
Exon 1.3 (A:36-79 | B:36-79)
Exon 1.4 (A:79-129 | B:79-129)
Exon 1.5 (A:129-155 | B:129-155)
Exon 1.7 (A:155-172 | B:155-168)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.7
6: Boundary 1.7/1.8
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
ENST00000162749
1
ENSE00001044275
chr12:
6451261-6450942
320
TNR1A_HUMAN
1-13
13
0
-
-
1.2
ENST00000162749
2
ENSE00000714951
chr12:
6443410-6443257
154
TNR1A_HUMAN
14-65
52
2
A:13-36
B:11-36
24
26
1.3
ENST00000162749
3
ENSE00000714950
chr12:
6443031-6442903
129
TNR1A_HUMAN
65-108
44
2
A:36-79
B:36-79
44
44
1.4
ENST00000162749
4
ENSE00000714949
chr12:
6442682-6442533
150
TNR1A_HUMAN
108-158
51
2
A:79-129
B:79-129
51
51
1.5
ENST00000162749
5
ENSE00000714948
chr12:
6442313-6442235
79
TNR1A_HUMAN
158-184
27
2
A:129-155
B:129-155
27
27
1.7
ENST00000162749
7
ENSE00000714947
chr12:
6440092-6440019
74
TNR1A_HUMAN
184-209
26
2
A:155-172
B:155-168
18
14
1.8
ENST00000162749
8
ENSE00000714946
chr12:
6439877-6439764
114
TNR1A_HUMAN
209-247
39
0
-
-
1.9
ENST00000162749
9
ENSE00000714944
chr12:
6439461-6439433
29
TNR1A_HUMAN
247-256
10
0
-
-
1.10
ENST00000162749
10
ENSE00000714943
chr12:
6439232-6438944
289
TNR1A_HUMAN
257-353
97
0
-
-
1.11
ENST00000162749
11
ENSE00000866894
chr12:
6438788-6437924
865
TNR1A_HUMAN
353-455
103
0
-
-
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1exta1 (A:13-71)
1b: SCOP_d1exta2 (A:72-115)
1c: SCOP_d1exta3 (A:116-172)
1d: SCOP_d1extb1 (B:11-71)
1e: SCOP_d1extb2 (B:72-115)
1f: SCOP_d1extb3 (B:116-168)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
TNF receptor-like
(25)
Superfamily
:
TNF receptor-like
(25)
Family
:
TNF receptor-like
(16)
Protein domain
:
Tumor necrosis factor (TNF) receptor
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1exta1
A:13-71
1b
d1exta2
A:72-115
1c
d1exta3
A:116-172
1d
d1extb1
B:11-71
1e
d1extb2
B:72-115
1f
d1extb3
B:116-168
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1extA02 (A:98-148)
1b: CATH_1extB01 (B:11-97)
1c: CATH_1extB02 (B:98-148)
1d: CATH_1extA01 (A:13-97)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Tumor Necrosis Factor Receptor, subunit A; domain 2
(17)
Homologous Superfamily
:
Tumor Necrosis Factor Receptor, subunit A, domain 2
(16)
Human (Homo sapiens)
(13)
1a
1extA02
A:98-148
1b
1extB01
B:11-97
1c
1extB02
B:98-148
1d
1extA01
A:13-97
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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Nucleic
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Protein & NOT PROSITE
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Asymmetric Unit 1
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