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.
3K24
Biol. Unit 2
Info
Asym.Unit (79 KB)
Biol.Unit 1 (37 KB)
Biol.Unit 2 (39 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 MATURE APO-CATHEPSIN L C25A MUTANT IN COMPLEX WITH GLN-LEU-ALA PEPTIDE
Authors
:
M. A. Adams-Cioaba, J. C. Krupa, J. S. Mort, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Gen Consortium (Sgc)
Date
:
29 Sep 09 (Deposition) - 23 Mar 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Co-Crystal, Substrate, Protease, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. A. Adams-Cioaba, J. C. Krupa, C. Xu, J. S. Mort, J. Min
Structural Basis For The Recognition And Cleavage Of Histon H3 By Cathepsin L.
Nat Commun V. 2 197 2011
[
close entry info
]
Hetero Components
(4, 6)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC6 (SOFTWARE)
6: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
SER B:105 , VAL B:106 , ALA B:107 , ASN B:108 , NDG B:222
BINDING SITE FOR RESIDUE NAG B 221
2
AC3
SOFTWARE
NAG B:221 , MAN B:223 , MAN B:224
BINDING SITE FOR RESIDUE NDG B 222
3
AC4
SOFTWARE
NDG B:222 , MAN B:224 , BMA B:225
BINDING SITE FOR RESIDUE MAN B 223
4
AC5
SOFTWARE
NDG B:222 , MAN B:223
BINDING SITE FOR RESIDUE MAN B 224
5
AC6
SOFTWARE
CYS A:98 , TYR A:100 , ASN A:101 , MAN B:223 , NDG B:226
BINDING SITE FOR RESIDUE BMA B 225
6
AC7
SOFTWARE
CYS A:98 , BMA B:225 , HOH B:238
BINDING SITE FOR RESIDUE NDG B 226
[
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: THIOL_PROTEASE_CYS (B:19-30)
2: THIOL_PROTEASE_HIS (B:161-171)
3: THIOL_PROTEASE_ASN (B:182-201)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOL_PROTEASE_CYS
PS00139
Eukaryotic thiol (cysteine) proteases cysteine active site.
CATL1_HUMAN
132-143
1
-
B:19-30
2
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATL1_HUMAN
274-284
1
-
B:161-171
3
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATL1_HUMAN
295-314
1
-
B:182-201
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3k24A00 (A:1-220)
1b: CATH_3k24B00 (B:1-220)
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
3k24A00
A:1-220
1b
3k24B00
B:1-220
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_C1_3k24B01 (B:1-219)
1b: PFAM_Peptidase_C1_3k24B02 (B:1-219)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_CA
(169)
Family
:
Peptidase_C1
(81)
Homo sapiens (Human)
(45)
1a
Peptidase_C1-3k24B01
B:1-219
1b
Peptidase_C1-3k24B02
B:1-219
[
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 C
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 (79 KB)
Header - Asym.Unit
Biol.Unit 1 (37 KB)
Header - Biol.Unit 1
Biol.Unit 2 (39 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
3K24
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help