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.
3FP6
Asym. Unit
Info
Asym.Unit (60 KB)
Biol.Unit 1 (55 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ANIONIC TRYPSIN IN COMPLEX WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) DETERMINED TO THE 1.49 A RESOLUTION LIMIT
Authors
:
E. Zakharova, M. P. Horvath, D. P. Goldenberg
Date
:
04 Jan 09 (Deposition) - 17 Feb 09 (Release) - 18 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.49
Chains
:
Asym. Unit : E,I
Biol. Unit 1: E,I (1x)
Keywords
:
Enzyme-Inhibitor Complex, Calcium, Digestion, Hydrolase, Metal-Binding, Protease, Secreted, Serine Protease, Zymogen, Pharmaceutical, Protease Inhibitor, Serine Protease Inhibitor, Hydrolase/Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Zakharova, M. P. Horvath, D. P. Goldenberg
Structure Of A Serine Protease Poised To Resynthesize A Peptide Bond.
Proc. Natl. Acad. Sci. Usa V. 106 11034 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 14)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
3a: TETRAETHYLENE GLYCOL (PG4a)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
3
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN E:34 , GLY E:38 , TYR E:39 , HIS E:40 , ARG E:67 , ILE E:73 , HOH E:709 , HOH E:718 , HOH E:779
BINDING SITE FOR RESIDUE EDO E 501
02
AC2
SOFTWARE
ASN E:100 , ASN E:101 , ASN E:179
BINDING SITE FOR RESIDUE EDO E 502
03
AC3
SOFTWARE
TYR E:59 , ILE E:88 , LYS E:90 , ASP E:236
BINDING SITE FOR RESIDUE EDO E 503
04
AC4
SOFTWARE
ASN E:143 , CYS E:191 , GLN E:192 , HOH E:784 , HOH E:884 , HOH E:890 , VAL I:34
BINDING SITE FOR RESIDUE EDO E 504
05
AC5
SOFTWARE
ILE E:47 , ASN E:48 , LEU E:123 , GLN E:239 , HOH E:823 , HOH E:830
BINDING SITE FOR RESIDUE EDO E 505
06
AC6
SOFTWARE
LYS E:97 , THR E:98 , TRP E:215 , TYR E:217 , HOH E:864 , HOH E:900
BINDING SITE FOR RESIDUE EDO E 506
07
AC7
SOFTWARE
TYR E:217 , GLY E:219 , HOH E:895 , ASP I:3 , TYR I:10 , GLY I:12 , PRO I:13 , EDO I:508 , HOH I:713
BINDING SITE FOR RESIDUE EDO E 507
08
AC8
SOFTWARE
GLY E:18 , PHE E:184A , GLU E:186 , GLY E:187 , GLY E:188 , LYS E:188A , HOH E:911
BINDING SITE FOR RESIDUE PG4 E 509
09
AC9
SOFTWARE
GLU E:70 , ASN E:72 , VAL E:75 , GLU E:77 , GLU E:80 , HOH E:776
BINDING SITE FOR RESIDUE CA E 601
10
BC1
SOFTWARE
LYS E:175 , HOH E:858 , HOH E:900 , ARG I:39 , ARG I:42 , HOH I:718
BINDING SITE FOR RESIDUE SO4 E 602
11
BC2
SOFTWARE
EDO E:507 , ASP I:3 , PHE I:4 , TYR I:10 , LYS I:41 , SO4 I:605
BINDING SITE FOR RESIDUE EDO I 508
12
BC3
SOFTWARE
ARG I:20 , TYR I:35 , ALA I:40 , HOH I:717 , HOH I:741 , HOH I:748 , HOH I:751 , HOH I:752
BINDING SITE FOR RESIDUE SO4 I 603
13
BC4
SOFTWARE
LYS E:60 , HOH E:751 , HOH E:852 , ILE I:18 , ILE I:19 , ARG I:20 , HOH I:742 , HOH I:761 , HOH I:763
BINDING SITE FOR RESIDUE SO4 I 604
14
BC5
SOFTWARE
LYS I:41 , ARG I:42 , EDO I:508 , HOH I:701 , HOH I:708 , HOH I:730 , HOH I:731
BINDING SITE FOR RESIDUE SO4 I 605
[
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, 5)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (E:16-243)
2: BPTI_KUNITZ_2 (I:5-55)
3: TRYPSIN_HIS (E:53-58)
4: BPTI_KUNITZ_1 (I:33-51)
5: TRYPSIN_SER (E: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
E:16-243
2
BPTI_KUNITZ_2
PS50279
Pancreatic trypsin inhibitor (Kunitz) family profile.
BPT1_BOVIN
40-90
1
I:5-55
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
TRY2_RAT
59-64
1
E:53-58
4
BPTI_KUNITZ_1
PS00280
Pancreatic trypsin inhibitor (Kunitz) family signature.
BPT1_BOVIN
68-86
1
I:33-51
5
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
TRY2_RAT
194-205
1
E:189-200
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.2b (E:16-61 (gaps))
Exon 1.3 (E:61-149 (gaps))
Exon 1.4 (E:149-192)
Exon 1.5 (E: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
E:16-61 (gaps)
46
1.3
ENSRNOT00000018852
3
ENSRNOE00000105498
chr4:
69092114-69092367
254
TRY2_RAT
67-152
86
1
E:61-149 (gaps)
89
1.4
ENSRNOT00000018852
4
ENSRNOE00000338303
chr4:
69092772-69092908
137
TRY2_RAT
152-197
46
1
E:149-192
46
1.5
ENSRNOT00000018852
5
ENSRNOE00000134316
chr4:
69093163-69093367
205
TRY2_RAT
198-246
49
1
E:193-245 (gaps)
54
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3fp6e_ (E:)
2a: SCOP_d3fp6i_ (I:)
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
d3fp6e_
E:
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
d3fp6i_
I:
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_3fp6I00 (I:1-58)
2a: CATH_3fp6E01 (E:16-27,E:121-232)
2b: CATH_3fp6E02 (E:28-120,E:233-245)
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)
Brown rat,rat,rats (Rattus norvegicus)
(2)
1a
3fp6I00
I:1-58
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Brown rat,rat,rats (Rattus norvegicus)
(3)
2a
3fp6E01
E:16-27,E:121-232
2b
3fp6E02
E:28-120,E: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 E
Chain I
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 (60 KB)
Header - Asym.Unit
Biol.Unit 1 (55 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
3FP6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
