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.
1KN9
Biol. Unit 2
Info
Asym.Unit (151 KB)
Biol.Unit 1 (41 KB)
Biol.Unit 2 (38 KB)
Biol.Unit 3 (41 KB)
Biol.Unit 4 (37 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 BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.
Authors
:
M. Paetzel, R. E. Dalbey, N. C. J. Strynadka
Date
:
18 Dec 01 (Deposition) - 30 Jan 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Serine Protease, Lysine General Base, Membrane Protein, Mostly Beta-Fold, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Paetzel, R. E. Dalbey, N. C. J. Strynadka
Crystal Structure Of A Bacterial Signal Peptidase Apoenzyme: Implications For Signal Peptide Binding And The Ser-Lys Dyad Mechanism
J. Biol. Chem. V. 277 9512 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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: SPASE_I_1 (B:88-95)
2: SPASE_I_2 (B:145-157)
3: SPASE_I_3 (B:268-281)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SPASE_I_1
PS00501
Signal peptidases I serine active site.
LEP_ECOLI
89-96
1
-
B:88-95
-
-
2
SPASE_I_2
PS00760
Signal peptidases I lysine active site.
LEP_ECOLI
146-158
1
-
B:145-157
-
-
3
SPASE_I_3
PS00761
Signal peptidases I signature 3.
LEP_ECOLI
269-282
1
-
B:268-281
-
-
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1kn9a_ (A:)
1b: SCOP_d1kn9b_ (B:)
1c: SCOP_d1kn9c_ (C:)
1d: SCOP_d1kn9d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
LexA/Signal peptidase
(17)
Superfamily
:
LexA/Signal peptidase
(17)
Family
:
Type 1 signal peptidase
(5)
Protein domain
:
Type 1 signal peptidase
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d1kn9a_
A:
1b
d1kn9b_
B:
1c
d1kn9c_
C:
1d
d1kn9d_
D:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1kn9B02 (B:154-188,B:224-262)
1b: CATH_1kn9D02 (D:154-188,D:224-262)
1c: CATH_1kn9A02 (A:154-188,A:224-262)
1d: CATH_1kn9C02 (C:154-188,C:224-262)
2a: CATH_1kn9B01 (B:78-153,B:263-319)
2b: CATH_1kn9D01 (D:78-153,D:263-319)
2c: CATH_1kn9A01 (A:76-153,A:263-323)
2d: CATH_1kn9C01 (C:76-153,C:263-323)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Signal Peptidase I; Chain: A, domain 2
(4)
Homologous Superfamily
:
[code=2.170.230.10, no name defined]
(4)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(1)
1a
1kn9B02
B:154-188,B:224-262
1b
1kn9D02
D:154-188,D:224-262
1c
1kn9A02
A:154-188,A:224-262
1d
1kn9C02
C:154-188,C:224-262
Architecture
:
Ribbon
(789)
Topology
:
Umud Fragment, subunit A
(13)
Homologous Superfamily
:
Umud Fragment, subunit A
(13)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(1)
2a
1kn9B01
B:78-153,B:263-319
2b
1kn9D01
D:78-153,D:263-319
2c
1kn9A01
A:76-153,A:263-323
2d
1kn9C01
C:76-153,C:263-323
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_S24_1kn9D01 (D:85-169)
1b: PFAM_Peptidase_S24_1kn9D02 (D:85-169)
1c: PFAM_Peptidase_S24_1kn9D03 (D:85-169)
1d: PFAM_Peptidase_S24_1kn9D04 (D:85-169)
2a: PFAM_Peptidase_S26_1kn9D05 (D:232-301)
2b: PFAM_Peptidase_S26_1kn9D06 (D:232-301)
2c: PFAM_Peptidase_S26_1kn9D07 (D:232-301)
2d: PFAM_Peptidase_S26_1kn9D08 (D:232-301)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_SF
(8)
Family
:
Peptidase_S24
(8)
Escherichia coli (strain K12)
(7)
1a
Peptidase_S24-1kn9D01
D:85-169
1b
Peptidase_S24-1kn9D02
D:85-169
1c
Peptidase_S24-1kn9D03
D:85-169
1d
Peptidase_S24-1kn9D04
D:85-169
Family
:
Peptidase_S26
(1)
Escherichia coli (strain K12)
(1)
2a
Peptidase_S26-1kn9D05
D:232-301
2b
Peptidase_S26-1kn9D06
D:232-301
2c
Peptidase_S26-1kn9D07
D:232-301
2d
Peptidase_S26-1kn9D08
D:232-301
[
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 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 (151 KB)
Header - Asym.Unit
Biol.Unit 1 (41 KB)
Header - Biol.Unit 1
Biol.Unit 2 (38 KB)
Header - Biol.Unit 2
Biol.Unit 3 (41 KB)
Header - Biol.Unit 3
Biol.Unit 4 (37 KB)
Header - Biol.Unit 4
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
1KN9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help