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Getting 'Biological Unit' information from database.
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3IT8
Biol. Unit 1
Info
Asym.Unit (437 KB)
Biol.Unit 1 (218 KB)
Biol.Unit 2 (217 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TNF ALPHA COMPLEXED WITH A POXVIRUS MHC-RELATED TNF BINDING PROTEIN
Authors
:
Z. Yang, A. P. West Jr. , P. J. Bjorkman
Date
:
27 Aug 09 (Deposition) - 20 Oct 09 (Release) - 09 Dec 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Mhc Class I Homolog, Cell Membrane, Cytokine, Disulfide Bond, Glycoprotein, Lipoprotein, Membrane, Myristate, Phosphoprotein, Secreted, Signal-Anchor, Transmembrane, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
Z. Yang, A. P. West, P. J. Bjorkman
Crystal Structure Of Tnfalpha Complexed With A Poxvirus Mhc-Related Tnf Binding Protein
Nat. Struct. Mol. Biol. V. 16 1189 2009
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Hetero Components
(1, 9)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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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: BC2 (SOFTWARE)
11: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS D:4 , ASN D:6 , THR D:8 , TYR D:22 , HOH D:328
BINDING SITE FOR RESIDUE NAG D 325
02
AC2
SOFTWARE
ASN D:52 , SER D:54 , ARG D:55
BINDING SITE FOR RESIDUE NAG D 326
03
AC3
SOFTWARE
ASN D:83
BINDING SITE FOR RESIDUE NAG D 327
04
AC4
SOFTWARE
LYS E:4 , ASN E:6 , THR E:8 , TYR E:22 , ILE E:94
BINDING SITE FOR RESIDUE NAG E 325
05
AC5
SOFTWARE
ASN E:52 , ARG E:55
BINDING SITE FOR RESIDUE NAG E 326
06
AC6
SOFTWARE
ASN E:83 , SER E:85
BINDING SITE FOR RESIDUE NAG E 327
07
AC7
SOFTWARE
LYS F:4 , ASN F:6 , THR F:8 , TYR F:22 , ILE F:94 , GLU F:111
BINDING SITE FOR RESIDUE NAG F 325
08
AC8
SOFTWARE
ASN F:52 , SER F:54 , ARG F:55
BINDING SITE FOR RESIDUE NAG F 326
09
AC9
SOFTWARE
ASN F:83
BINDING SITE FOR RESIDUE NAG F 327
10
BC2
SOFTWARE
PHE E:46 , ARG E:47 , ASN J:52 , ARG J:55
BINDING SITE FOR RESIDUE NAG J 326
11
BC9
SOFTWARE
TYR F:233 , ASN L:83
BINDING SITE FOR RESIDUE NAG L 327
[
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]
SAPs(SNPs)/Variants
(2, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_019378 (P8L, chain A/B/C, )
2: VAR_011927 (A18T, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_019378
P
84
L
TNFA_HUMAN
Polymorphism
4645843
A/B/C
P
8
L
2
UniProt
VAR_011927
A
94
T
TNFA_HUMAN
Polymorphism
1800620
A/B/C
A
18
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: TNF_2 (A:13-157,B:13-157,C:13-157)
2: TNF_1 (A:48-64,B:48-64,C:48-64)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNF_2
PS50049
TNF family profile.
TNFA_HUMAN
89-233
3
A:13-157
B:13-157
C:13-157
-
-
-
2
TNF_1
PS00251
TNF family signature.
TNFA_HUMAN
124-140
3
A:48-64
B:48-64
C:48-64
-
-
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3it8a_ (A:)
1b: SCOP_d3it8b_ (B:)
1c: SCOP_d3it8c_ (C:)
1d: SCOP_d3it8g_ (G:)
1e: SCOP_d3it8h_ (H:)
1f: SCOP_d3it8i_ (I:)
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Classes
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
automated matches
(12)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d3it8a_
A:
1b
d3it8b_
B:
1c
d3it8c_
C:
1d
d3it8g_
G:
1e
d3it8h_
H:
1f
d3it8i_
I:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3it8A00 (A:6-157)
1b: CATH_3it8B00 (B:6-157)
1c: CATH_3it8C00 (C:6-157)
1d: CATH_3it8G00 (G:6-157)
1e: CATH_3it8H00 (H:6-157)
1f: CATH_3it8I00 (I:6-157)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.40, no name defined]
(56)
Human (Homo sapiens)
(38)
1a
3it8A00
A:6-157
1b
3it8B00
B:6-157
1c
3it8C00
C:6-157
1d
3it8G00
G:6-157
1e
3it8H00
H:6-157
1f
3it8I00
I:6-157
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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Example Commands
Example Command
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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)
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Show PDB file:
Asym.Unit (437 KB)
Header - Asym.Unit
Biol.Unit 1 (218 KB)
Header - Biol.Unit 1
Biol.Unit 2 (217 KB)
Header - Biol.Unit 2
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