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.
1J17
Asym. Unit
Info
Asym.Unit (42 KB)
Biol.Unit 1 (38 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT
Authors
:
M. T. Stubbs
Date
:
30 Nov 02 (Deposition) - 23 Dec 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : T
Biol. Unit 1: T (1x)
Keywords
:
Serine Protease, Hydrolase, Serine Proteinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Reyda, C. Sohn, G. Klebe, K. Rall, D. Ullmann, H. D. Jakubke, M. T. Stubbs
Reconstructing The Binding Site Of Factor Xa In Trypsin Reveals Ligand-Induced Structural Plasticity
J. Mol. Biol. V. 325 963 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: SULFATE ION (SO4a)
3a: [4-(6-CHLORO-NAPHTHALENE-2-SULFONY... (ZENa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
SO4
1
Ligand/Ion
SULFATE ION
3
ZEN
1
Ligand/Ion
[4-(6-CHLORO-NAPHTHALENE-2-SULFONYL)-PIPERAZIN-1-YL]-(3,4,5,6-TETRAHYDRO-2H-[1,4']BIPYRIDINYL-4-YL)-METHANONE
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU T:70 , ASN T:72 , VAL T:75 , GLU T:77 , GLU T:80 , HOH T:261
BINDING SITE FOR RESIDUE CA T 480
2
AC2
SOFTWARE
ZEN T:1 , HIS T:57 , GLN T:192 , GLY T:193 , SER T:195 , HOH T:726
BINDING SITE FOR RESIDUE SO4 T 600
3
AC3
SOFTWARE
GLU T:97 , THR T:98 , TYR T:99 , LEU T:145 , GLY T:148 , VAL T:149 , PHE T:174 , ALA T:190 , GLN T:192 , SER T:195 , VAL T:213 , TRP T:215 , GLY T:216 , GLY T:219 , CYS T:220 , GLY T:226 , VAL T:227 , TYR T:228 , SO4 T:600 , HOH T:723 , HOH T:729
BINDING SITE FOR RESIDUE ZEN T 1
[
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (T:16-243)
2: TRYPSIN_HIS (T:53-58)
3: TRYPSIN_SER (T:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
TRY2_RAT
24-244
1
T:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
TRY2_RAT
59-64
1
T:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
TRY2_RAT
194-205
1
T:189-200
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.2b (T:16-61 (gaps))
Exon 1.3 (T:61-149 (gaps))
Exon 1.4 (T:149-192)
Exon 1.5 (T:193-245 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2b
2: Boundary 1.2b/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/-
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
ENSRNOT00000018852
1
ENSRNOE00000331572
chr4:
69088288-69088327
40
TRY2_RAT
1-14
14
0
-
-
1.2b
ENSRNOT00000018852
2b
ENSRNOE00000277233
chr4:
69090744-69090903
160
TRY2_RAT
14-67
54
1
T:16-61 (gaps)
46
1.3
ENSRNOT00000018852
3
ENSRNOE00000105498
chr4:
69092114-69092367
254
TRY2_RAT
67-152
86
1
T:61-149 (gaps)
89
1.4
ENSRNOT00000018852
4
ENSRNOE00000338303
chr4:
69092772-69092908
137
TRY2_RAT
152-197
46
1
T:149-192
46
1.5
ENSRNOT00000018852
5
ENSRNOE00000134316
chr4:
69093163-69093367
205
TRY2_RAT
198-246
49
1
T:193-245 (gaps)
54
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1j17t_ (T:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Trypsin(ogen)
(500)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(36)
1a
d1j17t_
T:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1j17T01 (T:16-27,T:121-232)
1b: CATH_1j17T02 (T:28-120,T:233-245)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Norway rat (Rattus norvegicus)
(18)
1a
1j17T01
T:16-27,T:121-232
1b
1j17T02
T:28-120,T:233-245
[
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 T
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 (42 KB)
Header - Asym.Unit
Biol.Unit 1 (38 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
1J17
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
