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.
1F9E
Biol. Unit 3
Info
Asym.Unit (249 KB)
Biol.Unit 1 (85 KB)
Biol.Unit 2 (85 KB)
Biol.Unit 3 (84 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO
Authors
:
H. Blanchard, M. Donepudi, M. Tschopp, L. Kodandapani, J. C. Wu, M. G. Gr
Date
:
10 Jul 00 (Deposition) - 10 Jul 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,Q,R,S,T,U,V
Biol. Unit 1: A,B,C,D,Q,R (1x)
Biol. Unit 2: E,F,G,H,S,T (1x)
Biol. Unit 3: I,J,K,L,U,V (1x)
Keywords
:
Cysteine Protease, Caspase-8, Flice, Mch5, Mach, Apoptosis, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Blanchard, M. Donepudi, M. Tschopp, L. Kodandapani, J. C. Wu, M. G. Grutter
Caspase-8 Specificity Probed At Subsite S(4): Crystal Structure Of The Caspase-8-Z-Devd-Cho Complex.
J. Mol. Biol. V. 302 9 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: ASPARTIC ALDEHYDE (ASAa)
1b: ASPARTIC ALDEHYDE (ASAb)
1c: ASPARTIC ALDEHYDE (ASAc)
1d: ASPARTIC ALDEHYDE (ASAd)
1e: ASPARTIC ALDEHYDE (ASAe)
1f: ASPARTIC ALDEHYDE (ASAf)
2a: BENZYL CHLOROCARBONATE (PHQa)
2b: BENZYL CHLOROCARBONATE (PHQb)
2c: BENZYL CHLOROCARBONATE (PHQc)
2d: BENZYL CHLOROCARBONATE (PHQd)
2e: BENZYL CHLOROCARBONATE (PHQe)
2f: BENZYL CHLOROCARBONATE (PHQf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ASA
2
Mod. Amino Acid
ASPARTIC ALDEHYDE
2
PHQ
2
Mod. Amino Acid
BENZYL CHLOROCARBONATE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
ARG I:177 , ARG I:179 , HIS I:237 , GLY I:238 , GLN I:283 , CYS I:285 , VAL J:338 , SER J:339 , TYR J:340 , ARG J:341 , ASN J:342 , PRO J:343 , TRP J:348
BINDING SITE FOR CHAIN U OF (PHQ)DEVD
2
AC6
SOFTWARE
ARG K:177 , ARG K:179 , HIS K:237 , GLY K:238 , GLN K:283 , CYS K:285 , SER L:339 , TYR L:340 , ARG L:341 , ASN L:342 , PRO L:343 , TRP L:348 , LYS L:381C
BINDING SITE FOR CHAIN V OF (PHQ)DEVD
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_020127 (H204H, chain I/K, )
2: VAR_014204 (R175BW, chain I/K, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020127
D
285
H
CASP8_HUMAN
Polymorphism
1045485
I/K
H
204
H
2
UniProt
VAR_014204
R
248
W
CASP8_HUMAN
Disease (CASP8D)
17860424
I/K
R
175B
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: CASPASE_P20 (I:161-289,K:161-289)
2: CASPASE_HIS (I:224-238,K:224-238)
3: CASPASE_CYS (I:276-287,K:276-287)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CASPASE_P20
PS50208
Caspase family p20 domain profile.
CASP8_HUMAN
232-364
2
-
-
-
-
I:161-289
K:161-289
2
CASPASE_HIS
PS01121
Caspase family histidine active site.
CASP8_HUMAN
304-318
2
-
-
-
-
I:224-238
K:224-238
3
CASPASE_CYS
PS01122
Caspase family cysteine active site.
CASP8_HUMAN
351-362
2
-
-
-
-
I:276-287
K:276-287
[
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1f9e_1 (A:,B:)
1b: SCOP_d1f9e_2 (C:,D:)
1c: SCOP_d1f9e_3 (E:,F:)
1d: SCOP_d1f9e_4 (G:,H:)
1e: SCOP_d1f9e_5 (I:,J:)
1f: SCOP_d1f9e_6 (K:,L:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Caspase-like
(92)
Superfamily
:
Caspase-like
(92)
Family
:
Caspase catalytic domain
(76)
Protein domain
:
Caspase-8
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1f9e.1
A:,B:
1b
d1f9e.2
C:,D:
1c
d1f9e.3
E:,F:
1d
d1f9e.4
G:,H:
1e
d1f9e.5
I:,J:
1f
d1f9e.6
K:,L:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1f9eA00 (A:149-299)
1b: CATH_1f9eC00 (C:149-299)
1c: CATH_1f9eE00 (E:149-299)
1d: CATH_1f9eG00 (G:149-299)
1e: CATH_1f9eI00 (I:149-299)
1f: CATH_1f9eK00 (K:149-299)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1460, no name defined]
(93)
Human (Homo sapiens)
(87)
1a
1f9eA00
A:149-299
1b
1f9eC00
C:149-299
1c
1f9eE00
E:149-299
1d
1f9eG00
G:149-299
1e
1f9eI00
I:149-299
1f
1f9eK00
K:149-299
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 I
Chain J
Chain K
Chain L
Chain U
Chain V
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 (249 KB)
Header - Asym.Unit
Biol.Unit 1 (85 KB)
Header - Biol.Unit 1
Biol.Unit 2 (85 KB)
Header - Biol.Unit 2
Biol.Unit 3 (84 KB)
Header - Biol.Unit 3
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
1F9E
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help