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.
3K9M
Biol. Unit 2
Info
Asym.Unit (119 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (59 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CATHEPSIN B IN COMPLEX WITH STEFIN A
Authors
:
M. Renko, D. Turk
Date
:
16 Oct 09 (Deposition) - 03 Nov 09 (Release) - 05 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.61
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Disulfide Bond, Glycoprotein, Lysosome, Protease, Thiol Protease, Zymogen, Thiol Protease Inhibitor, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Renko, U. Pozgan, D. Majera, D. Turk
Stefin A Displaces The Occluding Loop Of Cathepsin B Only B As Much As Required To Bind To The Active Site Cleft
Febs J. V. 277 4338 2010
[
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
(3, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_051512 (P12L, chain B, )
2: VAR_048851 (T96M, chain D, )
3: VAR_014696 (S156N, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051512
P
91
L
CATB_HUMAN
Polymorphism
11548596
B
P
12
L
2
UniProt
VAR_048851
T
96
M
CYTA_HUMAN
Polymorphism
34173813
D
T
96
M
3
UniProt
VAR_014696
S
235
N
CATB_HUMAN
Polymorphism
17573
B
S
156
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: CYSTATIN (D:45-58)
2: THIOL_PROTEASE_CYS (B:23-34)
3: THIOL_PROTEASE_HIS (B:197-207)
4: THIOL_PROTEASE_ASN (B:214-233)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYSTATIN
PS00287
Cysteine proteases inhibitors signature.
CYTA_HUMAN
45-58
1
-
D:45-58
2
THIOL_PROTEASE_CYS
PS00139
Eukaryotic thiol (cysteine) proteases cysteine active site.
CATB_HUMAN
102-113
1
-
B:23-34
3
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATB_HUMAN
276-286
1
-
B:197-207
4
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATB_HUMAN
293-312
1
-
B:214-233
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d3k9mc_ (C:)
1b: SCOP_d3k9md_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
Cystatin/monellin
(68)
Family
:
Cystatins
(31)
Protein domain
:
Cystatin A (stefin A)
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d3k9mc_
C:
1b
d3k9md_
D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3k9mA00 (A:1-254)
1b: CATH_3k9mB00 (B:1-254)
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)
Human (Homo sapiens)
(92)
1a
3k9mA00
A:1-254
1b
3k9mB00
B:1-254
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Cystatin_3k9mD01 (D:4-92)
1b: PFAM_Cystatin_3k9mD02 (D:4-92)
2a: PFAM_Peptidase_C1_3k9mB01 (B:1-250)
2b: PFAM_Peptidase_C1_3k9mB02 (B:1-250)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cystatin
(20)
Family
:
Cystatin
(15)
Homo sapiens (Human)
(12)
1a
Cystatin-3k9mD01
D:4-92
1b
Cystatin-3k9mD02
D:4-92
Clan
:
Peptidase_CA
(169)
Family
:
Peptidase_C1
(81)
Homo sapiens (Human)
(45)
2a
Peptidase_C1-3k9mB01
B:1-250
2b
Peptidase_C1-3k9mB02
B:1-250
[
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 B
Chain D
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 (119 KB)
Header - Asym.Unit
Biol.Unit 1 (58 KB)
Header - Biol.Unit 1
Biol.Unit 2 (59 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
3K9M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help