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.
1NPZ
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (38 KB)
Biol.Unit 2 (38 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURES OF CATHEPSIN S INHIBITOR COMPLEXES
Authors
:
T. A. Pauly, T. Sulea, M. Ammirati, J. Sivaraman, D. E. Danley, M. C. Grif A. V. Kamath, I. K. Wang, E. R. Laird, A. P. Seddon, R. Menard, M. Cygler,
Date
:
20 Jan 03 (Deposition) - 15 Apr 03 (Release) - 07 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Antigen Presentation, Binding Specificity, Cysteine Proteases, Inhibitor Complexes, Structure-Based Design, Structural Plasticity, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. A. Pauly, T. Sulea, M. Ammirati, J. Sivaraman, D. E. Danley, M. C. Griffor, A. V. Kamath, I. K. Wang, E. R. Laird, A. P. Seddon, R. Menard, M. Cygler, V. L. Rath
Specificity Determinants Of Human Cathepsin S Revealed By Crystal Structures Of Complexes.
Biochemistry V. 42 3203 2003
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: N~2~-(MORPHOLIN-4-YLCARBONYL)-N-[(... (C1Pa)
1b: N~2~-(MORPHOLIN-4-YLCARBONYL)-N-[(... (C1Pb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C1P
2
Ligand/Ion
N~2~-(MORPHOLIN-4-YLCARBONYL)-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-LEUCINAMIDE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:19 , GLY A:23 , CYS A:25 , TRP A:26 , ASN A:67 , GLY A:68 , GLY A:69 , PHE A:70 , ALA A:140 , TYR A:154 , ASN A:163 , HIS A:164 , TRP A:186 , HOH A:628 , PHE B:396 , LEU B:397
BINDING SITE FOR RESIDUE C1P A 468
2
AC2
SOFTWARE
PHE A:146 , LEU A:147 , GLN B:269 , GLY B:273 , CYS B:275 , TRP B:276 , CYS B:316 , ASN B:317 , GLY B:318 , GLY B:319 , PHE B:320 , ALA B:390 , VAL B:412 , ASN B:413 , HIS B:414 , TRP B:436
BINDING SITE FOR RESIDUE C1P B 469
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_025386 (T297T, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_025386
S
161
T
CATS_HUMAN
Polymorphism
1059604
A
B
T
47
297
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: THIOL_PROTEASE_CYS (A:19-30,B:269-280)
2: THIOL_PROTEASE_HIS (A:162-172,B:412-422)
3: THIOL_PROTEASE_ASN (A:179-198,B:429-448)
;
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.
CATS_HUMAN
133-144
2
A:19-30
B:269-280
2
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATS_HUMAN
276-286
2
A:162-172
B:412-422
3
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATS_HUMAN
293-312
2
A:179-198
B:429-448
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.4 (A:1-19 | B:251-269)
Exon 1.5a (A:20-95 | B:270-345)
Exon 1.6b (A:96-151 | B:346-401)
Exon 1.8b (A:151-185 | B:401-435)
Exon 1.9c (A:185-217 | B:435-467)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.4
2: Boundary 1.4/1.5a
3: Boundary 1.5a/1.6b
4: Boundary 1.6b/1.8b
5: Boundary 1.8b/1.9c
6: Boundary 1.9c/-
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
ENST00000368985
1a
ENSE00001922877
chr1:
150738433-150738174
260
CATS_HUMAN
-
0
0
-
-
1.2a
ENST00000368985
2a
ENSE00001448523
chr1:
150737240-150737114
127
CATS_HUMAN
1-42
42
0
-
-
1.3
ENST00000368985
3
ENSE00001044461
chr1:
150730456-150730334
123
CATS_HUMAN
43-83
41
0
-
-
1.4
ENST00000368985
4
ENSE00001044451
chr1:
150727626-150727477
150
CATS_HUMAN
84-133
50
2
A:1-19
B:251-269
19
19
1.5a
ENST00000368985
5a
ENSE00001044460
chr1:
150724484-150724257
228
CATS_HUMAN
134-209
76
2
A:20-95
B:270-345
76
76
1.6b
ENST00000368985
6b
ENSE00001044464
chr1:
150722647-150722482
166
CATS_HUMAN
210-265
56
2
A:96-151
B:346-401
56
56
1.8b
ENST00000368985
8b
ENSE00001044458
chr1:
150720355-150720253
103
CATS_HUMAN
265-299
35
2
A:151-185
B:401-435
35
35
1.9c
ENST00000368985
9c
ENSE00001874248
chr1:
150705621-150702672
2950
CATS_HUMAN
299-331
33
2
A:185-217
B:435-467
33
33
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1npza_ (A:)
1b: SCOP_d1npzb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Papain-like
(200)
Protein domain
:
(Pro)cathepsin S
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
1a
d1npza_
A:
1b
d1npzb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1npzA00 (A:1-217)
1b: CATH_1npzB00 (B:251-467)
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
1npzA00
A:1-217
1b
1npzB00
B:251-467
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_C1_1npzB01 (B:251-466)
1b: PFAM_Peptidase_C1_1npzB02 (B:251-466)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_CA
(169)
Family
:
Peptidase_C1
(81)
Homo sapiens (Human)
(45)
1a
Peptidase_C1-1npzB01
B:251-466
1b
Peptidase_C1-1npzB02
B:251-466
[
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 (78 KB)
Header - Asym.Unit
Biol.Unit 1 (38 KB)
Header - Biol.Unit 1
Biol.Unit 2 (38 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
1NPZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help