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.
PLEASE WAIT...
Getting 'Exon' information from database.
1DF0
Asym. Unit
Info
Asym.Unit (146 KB)
Biol.Unit 1 (140 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 M-CALPAIN
Authors
:
C. M. Hosfield, J. S. Elce, P. L. Davies, Z. Jia
Date
:
16 Nov 99 (Deposition) - 21 Jun 00 (Release) - 09 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cysteine Protease, Calmodulin, Papain, Catalytic Triad, Zymogen Activation, C2 Domain, Protease, Zymogen, Calpain, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. M. Hosfield, J. S. Elce, P. L. Davies, Z. Jia
Crystal Structure Of Calpain Reveals The Structural Basis For Ca(2+)-Dependent Protease Activity And A Novel Mode Of Enzyme Activation.
Embo J. V. 18 6880 1999
(for further references see the
PDB file header
)
[
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 not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 12)
Info
All PROSITE Patterns/Profiles
1: CALPAIN_CAT (A:45-344)
2: THIOL_PROTEASE_CYS (A:99-110)
3: EF_HAND_1 (B:68-80|B:98-110,A:585-597|A:615-6...)
4: EF_HAND_2 (B:85-120|B:55-83|B:150-184,A:602-6...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CALPAIN_CAT
PS50203
Cysteine proteinase, calpain-type, catalytic domain profile.
CAN2_RAT
45-344
1
A:45-344
2
THIOL_PROTEASE_CYS
PS00139
Eukaryotic thiol (cysteine) proteases cysteine active site.
CAN2_RAT
99-110
1
A:99-110
3
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
CPNS1_RAT
154-166
184-196
2
B:68-80
B:98-110
CAN2_RAT
585-597
615-627
2
A:585-597
A:615-627
4
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
CPNS1_RAT
171-206
141-169
236-270
3
B:85-120
B:55-83
B:150-184
CAN2_RAT
602-637
572-597
667-700
3
A:602-637
A:572-597
A:667-700
[
close PROSITE info
]
Exons
(21, 21)
Info
All Exons
Exon 1.1 (A:2-79)
Exon 1.2 (A:80-103)
Exon 1.3 (A:103-142)
Exon 1.4 (A:143-187)
Exon 1.5 (A:187-243)
Exon 1.6 (A:244-271 (gaps))
Exon 1.7 (A:272-290 (gaps))
Exon 1.8 (A:322-325)
Exon 1.9 (A:325-379)
Exon 1.10 (A:379-435 (gaps))
Exon 1.11 (A:436-436)
Exon 1.12 (A:449-510 (gaps))
Exon 1.13 (A:510-522)
Exon 1.14 (A:523-544 (gaps))
Exon 1.15 (A:545-563)
Exon 1.16 (A:568-585)
Exon 1.17 (A:586-608)
Exon 1.18 (A:609-635)
Exon 1.19 (A:635-674)
Exon 1.20 (A:674-693)
Exon 1.21 (A:694-700)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/1.15
16: Boundary 1.15/1.16
17: Boundary 1.16/1.17
18: Boundary 1.17/1.18
19: Boundary 1.18/1.19
20: Boundary 1.19/1.20
21: Boundary 1.20/1.21
22: Boundary 1.21/-
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
ENSRNOT00000045326
1
ENSRNOE00000309023
chr13:
98524463-98523801
663
CAN2_RAT
1-79
79
1
A:2-79
78
1.2
ENSRNOT00000045326
2
ENSRNOE00000302168
chr13:
98519114-98519045
70
CAN2_RAT
80-103
24
1
A:80-103
24
1.3
ENSRNOT00000045326
3
ENSRNOE00000304443
chr13:
98499555-98499437
119
CAN2_RAT
103-142
40
1
A:103-142
40
1.4
ENSRNOT00000045326
4
ENSRNOE00000339353
chr13:
98498897-98498764
134
CAN2_RAT
143-187
45
1
A:143-187
45
1.5
ENSRNOT00000045326
5
ENSRNOE00000333421
chr13:
98497787-98497619
169
CAN2_RAT
187-243
57
1
A:187-243
57
1.6
ENSRNOT00000045326
6
ENSRNOE00000031098
chr13:
98496708-98496625
84
CAN2_RAT
244-271
28
1
A:244-271 (gaps)
28
1.7
ENSRNOT00000045326
7
ENSRNOE00000279872
chr13:
98495644-98495559
86
CAN2_RAT
272-300
29
1
A:272-290 (gaps)
19
1.8
ENSRNOT00000045326
8
ENSRNOE00000320842
chr13:
98494333-98494259
75
CAN2_RAT
300-325
26
1
A:322-325
4
1.9
ENSRNOT00000045326
9
ENSRNOE00000314027
chr13:
98493169-98493009
161
CAN2_RAT
325-379
55
1
A:325-379
55
1.10
ENSRNOT00000045326
10
ENSRNOE00000314940
chr13:
98491026-98490857
170
CAN2_RAT
379-435
57
1
A:379-435 (gaps)
57
1.11
ENSRNOT00000045326
11
ENSRNOE00000427163
chr13:
98489237-98489226
12
CAN2_RAT
436-439
4
1
A:436-436
1
1.12
ENSRNOT00000045326
12
ENSRNOE00000362195
chr13:
98488354-98488143
212
CAN2_RAT
440-510
71
1
A:449-510 (gaps)
62
1.13
ENSRNOT00000045326
13
ENSRNOE00000299140
chr13:
98486485-98486449
37
CAN2_RAT
510-522
13
1
A:510-522
13
1.14
ENSRNOT00000045326
14
ENSRNOE00000031182
chr13:
98485176-98485111
66
CAN2_RAT
523-544
22
1
A:523-544 (gaps)
22
1.15
ENSRNOT00000045326
15
ENSRNOE00000349861
chr13:
98483613-98483556
58
CAN2_RAT
545-564
20
1
A:545-563
19
1.16
ENSRNOT00000045326
16
ENSRNOE00000321932
chr13:
98480438-98480374
65
CAN2_RAT
564-585
22
1
A:568-585
18
1.17
ENSRNOT00000045326
17
ENSRNOE00000031210
chr13:
98479391-98479323
69
CAN2_RAT
586-608
23
1
A:586-608
23
1.18
ENSRNOT00000045326
18
ENSRNOE00000341239
chr13:
98478952-98478874
79
CAN2_RAT
609-635
27
1
A:609-635
27
1.19
ENSRNOT00000045326
19
ENSRNOE00000343555
chr13:
98476968-98476852
117
CAN2_RAT
635-674
40
1
A:635-674
40
1.20
ENSRNOT00000045326
20
ENSRNOE00000365776
chr13:
98476397-98476339
59
CAN2_RAT
674-693
20
1
A:674-693
20
1.21
ENSRNOT00000045326
21
ENSRNOE00000423005
chr13:
98474374-98473368
1007
CAN2_RAT
694-700
7
1
A:694-700
7
[
close EXON info
]
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1df0a1 (A:515-700)
2a: SCOP_d1df0b_ (B:)
3a: SCOP_d1df0a2 (A:356-514)
4a: SCOP_d1df0a3 (A:2-355)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Penta-EF-hand proteins
(30)
Protein domain
:
Calpain large subunit, C-terminal domain (domain IV)
(5)
Norway rat (Rattus norvegicus), M-type [TaxId: 10116]
(2)
1a
d1df0a1
A:515-700
Protein domain
:
Calpain small (regulatory) subunit (domain VI)
(16)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(8)
2a
d1df0b_
B:
Class
:
All beta proteins
(24004)
Fold
:
Calpain large subunit, middle domain (domain III)
(5)
Superfamily
:
Calpain large subunit, middle domain (domain III)
(5)
Family
:
Calpain large subunit, middle domain (domain III)
(5)
Protein domain
:
Calpain large subunit, middle domain (domain III)
(5)
Norway rat (Rattus norvegicus), M-type [TaxId: 10116]
(2)
3a
d1df0a2
A:356-514
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Calpain large subunit, catalytic domain (domain II)
(19)
Protein domain
:
Calpain large subunit, catalytic domain (domain II)
(19)
Norway rat (Rattus norvegicus), M-type [TaxId: 10116]
(3)
4a
d1df0a3
A:2-355
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_1df0A02 (A:210-354)
2a: CATH_1df0B00 (B:9-184)
2b: CATH_1df0A04 (A:530-700)
3a: CATH_1df0A03 (A:355-505)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Cathepsin B; Chain A
(207)
Homologous Superfamily
:
Cysteine proteinases
(207)
Norway rat (Rattus norvegicus)
(6)
1a
1df0A02
A:210-354
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Norway rat (Rattus norvegicus)
(37)
2a
1df0B00
B:9-184
2b
1df0A04
A:530-700
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.380, no name defined]
(11)
Norway rat (Rattus norvegicus)
(3)
3a
1df0A03
A:355-505
[
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 A
Chain B
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 (146 KB)
Header - Asym.Unit
Biol.Unit 1 (140 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
1DF0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help