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.
PLEASE WAIT...
Getting 'Exon' information from database.
1PYO
Asym. Unit
Info
Asym.Unit (99 KB)
Biol.Unit 1 (94 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CASPASE-2 IN COMPLEX WITH ACETYL-LEU-ASP-GLU-SER-ASP-CHO
Authors
:
A. Schweizer, C. Briand, M. G. Grutter
Date
:
09 Jul 03 (Deposition) - 26 Aug 03 (Release) - 03 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Apoptosis, Caspase, Alpha-Beta, Thiol Protease, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Schweizer, C. Briand, M. G. Grutter
Crystal Structure Of Caspase-2, Apical Initiator Of The Intrinsic Apoptotic Pathway.
J. Biol. Chem. V. 278 42441 2003
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: (3S)-3-AMINO-4-HYDROXYBUTANOIC ACI... (ASJa)
2b: (3S)-3-AMINO-4-HYDROXYBUTANOIC ACI... (ASJb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
2
Mod. Amino Acid
ACETYL GROUP
2
ASJ
2
Mod. Amino Acid
(3S)-3-AMINO-4-HYDROXYBUTANOIC ACID
[
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
ASN B:232 , THR B:233 , TYR B:273 , LEU E:402
BINDING SITE FOR CHAIN E OF RESIDUES 401 TO 406
2
AC2
SOFTWARE
ASP B:269 , ASN D:232 , THR D:233 , LYS D:234 , LEU F:402
BINDING SITE FOR CHAIN F OF RESIDUES 401 TO 406
3
AC3
SOFTWARE
ARG A:54 , HIS A:112 , GLY A:113 , GLN A:153 , CYS A:155 , ALA B:228 , ALA B:229 , MET B:230 , ARG B:231 , ASN B:232 , THR B:233 , TRP B:238 , GLY B:272 , TYR B:273 , ALA B:274 , PHE B:279 , HOH B:345 , HOH E:383
BINDING SITE FOR CHAIN E OF ACETYL-LEU-ASP-GLU- SER-ASJ
4
AC4
SOFTWARE
GLN C:24 , ARG C:54 , HIS C:112 , GLY C:113 , GLN C:153 , CYS C:155 , HOH C:240 , ALA D:229 , MET D:230 , ARG D:231 , ASN D:232 , THR D:233 , TRP D:238 , GLY D:272 , TYR D:273 , PHE D:279 , ARG D:294 , HOH F:167 , HOH F:220 , HOH F:252 , HOH F:266
BINDING SITE FOR CHAIN F OF ACETYL-LEU-ASP-GLU- SER-ASJ
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016335 (P13A, chain A/C, )
2: VAR_016336 (R294G, chain B/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016335
P
178
A
CASP2_HUMAN
Polymorphism
4647298
A/C
P
13
A
2
UniProt
VAR_016336
R
441
G
CASP2_HUMAN
Polymorphism
4647338
B/D
R
294
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: CASPASE_P20 (A:33-159,C:33-159)
2: CASPASE_HIS (A:99-113,C:99-113)
3: CASPASE_CYS (A:146-157,C:146-157)
4: CASPASE_P10 (B:207-300,D:207-300)
;
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.
CASP2_HUMAN
198-324
2
A:33-159
C:33-159
2
CASPASE_HIS
PS01121
Caspase family histidine active site.
CASP2_HUMAN
264-278
2
A:99-113
C:99-113
3
CASPASE_CYS
PS01122
Caspase family cysteine active site.
CASP2_HUMAN
311-322
2
A:146-157
C:146-157
4
CASPASE_P10
PS50207
Caspase family p10 domain profile.
CASP2_HUMAN
354-447
2
B:207-300
D:207-300
[
close PROSITE info
]
Exons
(8, 18)
Info
All Exons
Exon 1.7a (A:9-25 | - | C:8-25 | -)
Exon 1.8a (A:26-84 | - | C:26-84 | -)
Exon 1.9 (A:85-127 | - | C:85-127 | -)
Exon 1.10a (A:128-158 | - | C:128-158 | -)
Exon 1.10e (A:158-167 | B:207-226 | C:158-168 ...)
Exon 1.11 (- | B:226-262 | - | D:226-262)
Exon 1.12d (- | B:263-304 | - | D:263-305)
Exon 2.1 (E:401-406 | F:401-406)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.5/1.7a
02: Boundary 1.7a/1.8a
03: Boundary 1.8a/1.9
04: Boundary 1.9/1.10a
05: Boundary 1.10a/1.10e
06: Boundary 1.10e/1.11
07: Boundary 1.11/1.12d
08: Boundary 1.12d/-
09: Boundary -/2.1
10: Boundary 2.1/-
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
1.1a
ENST00000310447
1a
ENSE00001809494
chr7:
142985308-142985622
315
CASP2_HUMAN
1-25
25
0
-
-
1.3a
ENST00000310447
3a
ENSE00001734851
chr7:
142988633-142988783
151
CASP2_HUMAN
25-75
51
0
-
-
1.4b
ENST00000310447
4b
ENSE00001363075
chr7:
142989393-142989560
168
CASP2_HUMAN
76-131
56
0
-
-
1.5
ENST00000310447
5
ENSE00000872252
chr7:
142989710-142989791
82
CASP2_HUMAN
132-159
28
0
-
-
1.7a
ENST00000310447
7a
ENSE00000728843
chr7:
142991323-142991417
95
CASP2_HUMAN
159-190
32
2
A:9-25
-
C:8-25
-
17
-
18
-
1.8a
ENST00000310447
8a
ENSE00001717071
chr7:
142991690-142991866
177
CASP2_HUMAN
191-249
59
2
A:26-84
-
C:26-84
-
59
-
59
-
1.9
ENST00000310447
9
ENSE00001734267
chr7:
142997016-142997144
129
CASP2_HUMAN
250-292
43
2
A:85-127
-
C:85-127
-
43
-
43
-
1.10a
ENST00000310447
10a
ENSE00001720132
chr7:
142997297-142997387
91
CASP2_HUMAN
293-323
31
2
A:128-158
-
C:128-158
-
31
-
31
-
1.10e
ENST00000310447
10e
ENSE00001802806
chr7:
143000877-143001026
150
CASP2_HUMAN
323-373
51
4
A:158-167
B:207-226
C:158-168
D:207-226
10
20
11
20
1.11
ENST00000310447
11
ENSE00001667926
chr7:
143001767-143001876
110
CASP2_HUMAN
373-409
37
2
-
B:226-262
-
D:226-262
-
37
-
37
1.12d
ENST00000310447
12d
ENSE00001823824
chr7:
143002033-143004789
2757
CASP2_HUMAN
410-452
43
2
-
B:263-304
-
D:263-305
-
42
-
43
2.1
YKR018C
1
YKR018C.1
XI:475543-473366
2178
YKR18_YEAST
1-725
725
2
E:401-406
F:401-406
6
6
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1pyo_1 (A:,B:)
1b: SCOP_d1pyo_2 (C:,D:)
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-2
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1pyo.1
A:,B:
1b
d1pyo.2
C:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1pyoC00 (C:8-168)
1b: CATH_1pyoA00 (A:9-167)
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
1pyoC00
C:8-168
1b
1pyoA00
A:9-167
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_C14_1pyoD01 (D:207-298)
1b: PFAM_Peptidase_C14_1pyoD02 (D:207-298)
1c: PFAM_Peptidase_C14_1pyoD03 (D:207-298)
1d: PFAM_Peptidase_C14_1pyoD04 (D:207-298)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_CD
(53)
Family
:
Peptidase_C14
(53)
Homo sapiens (Human)
(51)
1a
Peptidase_C14-1pyoD01
D:207-298
1b
Peptidase_C14-1pyoD02
D:207-298
1c
Peptidase_C14-1pyoD03
D:207-298
1d
Peptidase_C14-1pyoD04
D:207-298
[
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 A
Chain B
Chain C
Chain D
Chain E
Chain F
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 (99 KB)
Header - Asym.Unit
Biol.Unit 1 (94 KB)
Header - Biol.Unit 1
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
1PYO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help