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.
1P2N
Asym. Unit
Info
Asym.Unit (107 KB)
Biol.Unit 1 (53 KB)
Biol.Unit 2 (52 KB)
Biol.Unit 3 (103 KB)
Biol.Unit 4 (102 KB)
Biol.Unit 5 (53 KB)
Biol.Unit 6 (53 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL CONSEQUENCES OF ACCOMMODATION OF FOUR NON-COGNATE AMINO-ACID RESIDUES IN THE S1 POCKET OF BOVINE TRYPSIN AND CHYMOTRYPSIN
Authors
:
R. Helland, H. Czapinska, I. Leiros, M. Olufsen, J. Otlewski, A. O. Smalaas
Date
:
15 Apr 03 (Deposition) - 20 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
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)
Biol. Unit 4: A,B,C,D (1x)
Biol. Unit 5: B,C (1x)
Biol. Unit 6: A,D (1x)
Keywords
:
Trypsin; Chymotrypsin; Serine Proteinase; Bovine Pancreatic Trypsin Inhibitor; Protein-Protein Interaction; Non-Cognate Binding; S1 Pocket; Primary Specificity; Crystal Structure, Hydrolase/Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Helland, H. Czapinska, I. Leiros, M. Olufsen, J. Otlewski, A. O. Smalaas
Structural Consequences Of Accommodation Of Four Non-Cognate Amino Acid Residues In The S1 Pocket Of Bovine Trypsin And Chymotrypsin.
J. Mol. Biol. V. 333 845 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE B:4 , GLU B:7 , ARG B:42 , HOH B:2009 , HOH B:2315 , TYR D:10 , HOH D:2420
BINDING SITE FOR RESIDUE SO4 B 601
2
AC2
SOFTWARE
HOH A:660 , ARG B:20 , TYR B:35 , GLY B:37 , ALA B:40 , HOH B:671 , HOH B:682 , LEU C:97
BINDING SITE FOR RESIDUE SO4 B 602
3
AC3
SOFTWARE
TYR B:10 , HOH B:2251 , HOH B:2302 , HOH B:2481 , PHE D:4 , GLU D:7 , ARG D:42 , HOH D:2017
BINDING SITE FOR RESIDUE SO4 B 603
4
AC4
SOFTWARE
PRO B:2 , ASP B:3 , HOH B:2012 , HOH B:2065 , HOH B:2250 , HOH B:2338 , TYR C:171 , TRP C:172 , SER C:217 , SER C:218 , HOH C:2069
BINDING SITE FOR RESIDUE SO4 B 604
5
AC5
SOFTWARE
TYR A:171 , TRP A:172 , SER A:217 , SER A:218 , HOH A:2110 , HOH A:2247 , HOH A:2334 , PRO D:2 , ASP D:3 , HOH D:2013 , HOH D:2090
BINDING SITE FOR RESIDUE SO4 A 605
6
AC6
SOFTWARE
LEU A:97 , HOH C:1660 , ARG D:20 , TYR D:35 , GLY D:37 , HOH D:1671
BINDING SITE FOR RESIDUE SO4 D 1602
[
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
(5, 10)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (A:16-243,C:16-243)
2: BPTI_KUNITZ_2 (B:5-55,D:5-55)
3: TRYPSIN_HIS (A:53-58,C:53-58)
4: BPTI_KUNITZ_1 (B:33-51,D:33-51)
5: TRYPSIN_SER (A:189-200,C: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.
CTRA_BOVIN
16-243
2
A:16-243
C:16-243
2
BPTI_KUNITZ_2
PS50279
Pancreatic trypsin inhibitor (Kunitz) family profile.
BPT1_BOVIN
40-90
2
B:5-55
D:5-55
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
CTRA_BOVIN
53-58
2
A:53-58
C:53-58
4
BPTI_KUNITZ_1
PS00280
Pancreatic trypsin inhibitor (Kunitz) family signature.
BPT1_BOVIN
68-86
2
B:33-51
D:33-51
5
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
CTRA_BOVIN
189-200
2
A:189-200
C: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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1p2na_ (A:)
1b: SCOP_d1p2nc_ (C:)
2a: SCOP_d1p2nb_ (B:)
2b: SCOP_d1p2nd_ (D:)
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
:
(alpha,gamma)-chymotrypsin(ogen)
(60)
Cow (Bos taurus) [TaxId: 9913]
(58)
1a
d1p2na_
A:
1b
d1p2nc_
C:
Class
:
Small proteins
(3458)
Fold
:
BPTI-like
(161)
Superfamily
:
BPTI-like
(161)
Family
:
Small Kunitz-type inhibitors & BPTI-like toxins
(128)
Protein domain
:
Pancreatic trypsin inhibitor, BPTI
(85)
Cow (Bos taurus) [TaxId: 9913]
(85)
2a
d1p2nb_
B:
2b
d1p2nd_
D:
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1p2nB00 (B:1-58)
1b: CATH_1p2nD00 (D:1-58)
2a: CATH_1p2nA02 (A:28-120,A:233-243)
2b: CATH_1p2nC02 (C:28-120,C:233-243)
2c: CATH_1p2nA01 (A:16-27,A:121-232)
2d: CATH_1p2nC01 (C:16-27,C:121-232)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Factor Xa Inhibitor
(116)
Homologous Superfamily
:
Factor Xa Inhibitor
(116)
Cattle (Bos taurus)
(61)
1a
1p2nB00
B:1-58
1b
1p2nD00
D:1-58
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Cattle (Bos taurus)
(308)
2a
1p2nA02
A:28-120,A:233-243
2b
1p2nC02
C:28-120,C:233-243
2c
1p2nA01
A:16-27,A:121-232
2d
1p2nC01
C:16-27,C:121-232
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Trypsin_1p2nC01 (C:16-238)
1b: PFAM_Trypsin_1p2nC02 (C:16-238)
2a: PFAM_Kunitz_BPTI_1p2nD01 (D:4-56)
2b: PFAM_Kunitz_BPTI_1p2nD02 (D:4-56)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Bos taurus (Bovine)
(190)
1a
Trypsin-1p2nC01
C:16-238
1b
Trypsin-1p2nC02
C:16-238
Clan
:
Protease_inhib
(47)
Family
:
Kunitz_BPTI
(45)
Bos taurus (Bovine)
(33)
2a
Kunitz_BPTI-1p2nD01
D:4-56
2b
Kunitz_BPTI-1p2nD02
D:4-56
[
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
Chain C
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 (107 KB)
Header - Asym.Unit
Biol.Unit 1 (53 KB)
Header - Biol.Unit 1
Biol.Unit 2 (52 KB)
Header - Biol.Unit 2
Biol.Unit 3 (103 KB)
Header - Biol.Unit 3
Biol.Unit 4 (102 KB)
Header - Biol.Unit 4
Biol.Unit 5 (53 KB)
Header - Biol.Unit 5
Biol.Unit 6 (53 KB)
Header - Biol.Unit 6
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
1P2N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
