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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1ZA3
Biol. Unit 2
Info
Asym.Unit (175 KB)
Biol.Unit 1 (86 KB)
Biol.Unit 2 (83 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTAL STRUCTURE OF THE YSD1 FAB BOUND TO DR5
Authors
:
F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, S. S. Sid
Date
:
05 Apr 05 (Deposition) - 14 Jun 05 (Release) - 05 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.35
Chains
:
Asym. Unit : A,B,H,L,R,S
Biol. Unit 1: A,B,S (1x)
Biol. Unit 2: H,L,R (1x)
Keywords
:
Phage Display, Protein Engineering, Combinatorial Mutagenesis, Antibody Library, Death Receptor-5, Immune System-Signaling Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, S. S. Sidhu
Molecular Recognition By A Binary Code.
J. Mol. Biol. V. 348 1153 2005
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: TNFR_NGFR_2 (R:43-84)
2: TNFR_NGFR_1 (R:44-84)
;
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.
TR10B_HUMAN
96-137
138-178
2
R:43-84
-
R:85-123
-
2
TNFR_NGFR_1
PS00652
TNFR/NGFR family cysteine-rich region signature.
TR10B_HUMAN
97-137
137-178
2
R:44-84
-
R:84-123
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
(5, 14)
Info
All SCOP Domains
1a: SCOP_d1za3b2 (B:114-214)
1b: SCOP_d1za3h2 (H:114-214)
2a: SCOP_d1za3a2 (A:107-213)
2b: SCOP_d1za3l2 (L:107-213)
3a: SCOP_d1za3b1 (B:1-113)
3b: SCOP_d1za3h1 (H:1-113)
4a: SCOP_d1za3a1 (A:1-106)
4b: SCOP_d1za3l1 (L:1-106)
5a: SCOP_d1za3r1 (R:21-61)
5b: SCOP_d1za3r2 (R:62-101)
5c: SCOP_d1za3r3 (R:102-123)
5d: SCOP_d1za3s1 (S:21-61)
5e: SCOP_d1za3s2 (S:62-101)
5f: SCOP_d1za3s3 (S:102-123)
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
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
1a
d1za3b2
B:114-214
1b
d1za3h2
H:114-214
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1za3a2
A:107-213
2b
d1za3l2
L:107-213
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Camelid IG heavy chain variable domain, VHh
(28)
Human (Homo sapiens) [TaxId: 9606]
(2)
3a
d1za3b1
B:1-113
3b
d1za3h1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(9)
4a
d1za3a1
A:1-106
4b
d1za3l1
L:1-106
Class
:
Small proteins
(3458)
Fold
:
TNF receptor-like
(25)
Superfamily
:
TNF receptor-like
(25)
Family
:
TNF receptor-like
(16)
Protein domain
:
Death receptor-5 (dr5) fragment
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
5a
d1za3r1
R:21-61
5b
d1za3r2
R:62-101
5c
d1za3r3
R:102-123
5d
d1za3s1
S:21-61
5e
d1za3s2
S:62-101
5f
d1za3s3
S:102-123
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1za3R02 (R:62-101)
1b: CATH_1za3S02 (S:62-101)
1c: CATH_1za3R01 (R:21-61)
1d: CATH_1za3S01 (S:21-61)
2a: CATH_1za3A02 (A:108-213)
2b: CATH_1za3B02 (B:114-214)
2c: CATH_1za3H02 (H:114-214)
2d: CATH_1za3B01 (B:1-113)
2e: CATH_1za3H01 (H:1-113)
2f: CATH_1za3L02 (L:108-213)
2g: CATH_1za3A01 (A:1-107)
2h: CATH_1za3L01 (L:1-107)
View:
Select:
Label:
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)
[unclassified]
(1)
1a
1za3R02
R:62-101
1b
1za3S02
S:62-101
1c
1za3R01
R:21-61
1d
1za3S01
S:21-61
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
[unclassified]
(54)
2a
1za3A02
A:108-213
2b
1za3B02
B:114-214
2c
1za3H02
H:114-214
2d
1za3B01
B:1-113
2e
1za3H01
H:1-113
2f
1za3L02
L:108-213
2g
1za3A01
A:1-107
2h
1za3L01
L:1-107
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_TNFR_c6_1za3S01 (S:44-84)
1b: PFAM_TNFR_c6_1za3S02 (S:44-84)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: TNFR_c6]
(13)
Family
:
TNFR_c6
(13)
Homo sapiens (Human)
(8)
1a
TNFR_c6-1za3S01
S:44-84
1b
TNFR_c6-1za3S02
S:44-84
[
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 H
Chain L
Chain R
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 (175 KB)
Header - Asym.Unit
Biol.Unit 1 (86 KB)
Header - Biol.Unit 1
Biol.Unit 2 (83 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
1ZA3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
