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.
2A0Q
Biol. Unit 1
Info
Asym.Unit (103 KB)
Biol.Unit 1 (51 KB)
Biol.Unit 2 (50 KB)
Biol.Unit 3 (98 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THROMBIN IN 400 MM POTASSIUM CHLORIDE
Authors
:
M. Papaconstantinou, C. J. Carrell, A. O. Pineda, K. M. Bobofchak, F. S. Mathews, C. S. Flordellis, M. E. Maragoudakis, N. E. Tsopanoglou E. Di Cera
Date
:
16 Jun 05 (Deposition) - 12 Jul 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Serine Protease, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. E. Papaconstantinou, C. J. Carrell, A. O. Pineda, K. M. Bobofchak, F. S. Mathews, C. S. Flordellis, M. E. Maragoudakis, N. E. Tsopanoglou, E. Di Cera
Thrombin Functions Through Its Rgd Sequence In A Non-Canonical Conformation.
J. Biol. Chem. V. 280 29393 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
3a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
K
-1
Ligand/Ion
POTASSIUM ION
3
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN B:60G , HOH B:528
BINDING SITE FOR RESIDUE NDG B 401
2
AC2
SOFTWARE
HOH B:414 , ARG D:73 , GLY D:142 , ASN D:143
BINDING SITE FOR RESIDUE CL D 402
3
AC3
SOFTWARE
TYR B:184A , ARG B:221A , LYS B:224 , HOH B:409 , HOH B:434 , HOH B:510
BINDING SITE FOR RESIDUE K B 403
4
AC4
SOFTWARE
ASP B:221 , HOH B:420 , HOH B:476 , ILE D:16 , GLY D:142 , HOH D:447 , HOH D:472
BINDING SITE FOR RESIDUE K D 404
[
close Site info
]
SAPs(SNPs)/Variants
(7, 7)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_006714 (M32T, chain B, )
2: VAR_011782 (P37T, chain B, )
3: VAR_006715 (R67C, chain B, )
4: VAR_006716 (R73H, chain B, )
5: VAR_006717 (R101W, chain B, )
6: VAR_068913 (E164Q, chain B, )
7: VAR_006719 (G226V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006714
M
380
T
THRB_HUMAN
Disease (FA2D)
---
B
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
B
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
B
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
B
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
B
R
101
W
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
B
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
B
G
226
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (B:16-243)
2: TRYPSIN_HIS (B:53-58)
3: TRYPSIN_SER (B: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.
THRB_HUMAN
364-618
1
B:16-243
-
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
1
B:53-58
-
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
1
B:189-200
-
[
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, 4)
Info
all CATH domains
1a: CATH_2a0qB02 (B:28-120,B:233-244)
1b: CATH_2a0qB01 (B:16-27,B:121-232)
1c: CATH_2a0qD01 (D:16-27,D:121-232)
1d: CATH_2a0qD02 (D:28-120,D:233-244)
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)
Human (Homo sapiens)
(615)
1a
2a0qB02
B:28-120,B:233-244
1b
2a0qB01
B:16-27,B:121-232
1c
2a0qD01
D:16-27,D:121-232
1d
2a0qD02
D:28-120,D:233-244
[
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 (103 KB)
Header - Asym.Unit
Biol.Unit 1 (51 KB)
Header - Biol.Unit 1
Biol.Unit 2 (50 KB)
Header - Biol.Unit 2
Biol.Unit 3 (98 KB)
Header - Biol.Unit 3
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
2A0Q
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
