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.
2QYI
Asym. Unit
Info
Asym.Unit (134 KB)
Biol.Unit 1 (129 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 A BINARY COMPLEX BETWEEN AN ENGINEERED TRYPSIN INHIBITOR AND BOVINE TRYPSIN
Authors
:
S. Khamrui, J. Dasgupta, J. K. Dattagupta, U. Sen
Date
:
15 Aug 07 (Deposition) - 19 Aug 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
P1 Mutant, Trypsin Inhibitor, Bovine Trypsin, Complex, Calcium, Digestion, Hydrolase, Metal-Binding, Protease, Secreted, Serine Protease, Zymogen, Protease Inhibitor, Serine Protease Inhibitor, Hydrolase/Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Sen
Crystal Structure Of A Binary Complex Between An Engineered Trypsin Inhibitor And Bovine Trypsin
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: NICKEL (II) ION (NIa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
NI
1
Ligand/Ion
NICKEL (II) ION
[
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 A:70 , ASN A:72 , GLU A:80
BINDING SITE FOR RESIDUE CA A 991
2
AC2
SOFTWARE
HIS B:626 , HIS B:727 , GLU B:772 , HIS D:830
BINDING SITE FOR RESIDUE NI B 992
3
AC3
SOFTWARE
GLU C:370 , ASN C:372 , GLU C:380
BINDING SITE FOR RESIDUE CA C 990
[
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
(4, 8)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (A:16-243,C:316-543)
2: SOYBEAN_KUNITZ (B:607-623,D:807-823)
3: TRYPSIN_HIS (A:53-58,C:353-358)
4: TRYPSIN_SER (A:189-200,C:489-500)
;
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.
TRY1_BOVIN
24-244
2
A:16-243
C:316-543
2
SOYBEAN_KUNITZ
PS00283
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.
ICW3_PSOTE
28-44
2
B:607-623
D:807-823
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
TRY1_BOVIN
59-64
2
A:53-58
C:353-358
4
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
TRY1_BOVIN
194-205
2
A:189-200
C:489-500
[
close PROSITE info
]
Exons
(4, 8)
Info
All Exons
Exon 1.2 (A:16-63 (gaps) | C:316-363 (gaps))
Exon 1.3 (A:63-151 (gaps) | C:363-451 (gaps))
Exon 1.4 (A:151-194 | C:451-494)
Exon 1.5 (A:195-245 (gaps) | C:495-545 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
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
ENSBTAT00000033479
1
ENSBTAE00000401279
chr4:
109299627-109299547
81
TRY1_BOVIN
1-16
16
0
-
-
1.2
ENSBTAT00000033479
2
ENSBTAE00000397626
chr4:
109298170-109298011
160
TRY1_BOVIN
16-69
54
2
A:16-63 (gaps)
C:316-363 (gaps)
48
48
1.3
ENSBTAT00000033479
3
ENSBTAE00000409037
chr4:
109297593-109297340
254
TRY1_BOVIN
69-154
86
2
A:63-151 (gaps)
C:363-451 (gaps)
89
89
1.4
ENSBTAT00000033479
4
ENSBTAE00000386782
chr4:
109296654-109296518
137
TRY1_BOVIN
154-199
46
2
A:151-194
C:451-494
46
46
1.5
ENSBTAT00000033479
5
ENSBTAE00000422174
chr4:
109295990-109295749
242
TRY1_BOVIN
200-248
49
2
A:195-245 (gaps)
C:495-545 (gaps)
52
52
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2qyib_ (B:)
1b: SCOP_d2qyid_ (D:)
2a: SCOP_d2qyia_ (A:)
2b: SCOP_d2qyic_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
STI-like
(91)
Family
:
Kunitz (STI) inhibitors
(29)
Protein domain
:
chymotrypsin inhibitor WCI
(8)
Winged bean (Psophocarpus tetragonolobus) [TaxId: 3891]
(8)
1a
d2qyib_
B:
1b
d2qyid_
D:
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Trypsin(ogen)
(500)
Cow (Bos taurus) [TaxId: 9913]
(392)
2a
d2qyia_
A:
2b
d2qyic_
C:
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2qyiA01 (A:16-27,A:121-232)
1b: CATH_2qyiC01 (C:316-327,C:421-532)
1c: CATH_2qyiA02 (A:28-120,A:233-244)
1d: CATH_2qyiC02 (C:328-420,C:533-544)
2a: CATH_2qyiB00 (B:604-778)
2b: CATH_2qyiD00 (D:804-978)
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)
Bovine (Bos taurus)
(36)
1a
2qyiA01
A:16-27,A:121-232
1b
2qyiC01
C:316-327,C:421-532
1c
2qyiA02
A:28-120,A:233-244
1d
2qyiC02
C:328-420,C:533-544
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
Bovine (Bos taurus)
(2)
2a
2qyiB00
B:604-778
2b
2qyiD00
D:804-978
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Trypsin_2qyiC01 (C:316-538)
1b: PFAM_Trypsin_2qyiC02 (C:316-538)
2a: PFAM_Kunitz_legume_2qyiD01 (D:806-977)
2b: PFAM_Kunitz_legume_2qyiD02 (D:806-977)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Bos taurus (Bovine)
(190)
1a
Trypsin-2qyiC01
C:316-538
1b
Trypsin-2qyiC02
C:316-538
Clan
:
Trefoil
(131)
Family
:
Kunitz_legume
(9)
Psophocarpus tetragonolobus (Winged bean) (Dolichos tetragonolobus)
(6)
2a
Kunitz_legume-2qyiD01
D:806-977
2b
Kunitz_legume-2qyiD02
D:806-977
[
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 (134 KB)
Header - Asym.Unit
Biol.Unit 1 (129 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
2QYI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help