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.
1B12
Biol. Unit 1
Info
Asym.Unit (162 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (40 KB)
Biol.Unit 3 (42 KB)
Biol.Unit 4 (41 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 TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR
Authors
:
M. Paetzel, R. Dalbey, N. C. J. Strynadka
Date
:
24 Nov 99 (Deposition) - 10 Dec 99 (Release) - 09 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
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 Proteinase, Serine-Dependant Hydrolase, Signal Peptide Processing, Protein Translocation, Membrane Bound Proteinase, Membrane Protein, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Paetzel, R. E. Dalbey, N. C. Strynadka
Crystal Structure Of A Bacterial Signal Peptidase In Comple With A Beta-Lactam Inhibitor.
Nature V. 396 186 1998
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: PROP-2-EN-1-YL (2S)-2-[(2S,3R)-3-(... (1PNa)
1b: PROP-2-EN-1-YL (2S)-2-[(2S,3R)-3-(... (1PNb)
1c: PROP-2-EN-1-YL (2S)-2-[(2S,3R)-3-(... (1PNc)
1d: PROP-2-EN-1-YL (2S)-2-[(2S,3R)-3-(... (1PNd)
2a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PN
1
Ligand/Ion
PROP-2-EN-1-YL (2S)-2-[(2S,3R)-3-(ACETYLOXY)-1-OXOBUTAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLATE
2
PO4
-1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
ILE A:86 , PRO A:87 , SER A:88 , SER A:90 , TYR A:143 , ILE A:144 , LYS A:145 , SER A:278 , ALA A:279
BINDING SITE FOR RESIDUE 1PN A 1001
[
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 (A:88-95)
2: SPASE_I_2 (A:145-157)
3: SPASE_I_3 (A: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
A:88-95
-
-
-
2
SPASE_I_2
PS00760
Signal peptidases I lysine active site.
LEP_ECOLI
146-158
1
A:145-157
-
-
-
3
SPASE_I_3
PS00761
Signal peptidases I signature 3.
LEP_ECOLI
269-282
1
A: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_d1b12a_ (A:)
1b: SCOP_d1b12b_ (B:)
1c: SCOP_d1b12c_ (C:)
1d: SCOP_d1b12d_ (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
d1b12a_
A:
1b
d1b12b_
B:
1c
d1b12c_
C:
1d
d1b12d_
D:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1b12A02 (A:154-188,A:224-262)
1b: CATH_1b12C02 (C:154-188,C:224-262)
1c: CATH_1b12B02 (B:154-188,B:224-262)
1d: CATH_1b12D02 (D:154-188,D:224-262)
2a: CATH_1b12B01 (B:79-153,B:263-319)
2b: CATH_1b12C01 (C:78-153,C:263-321)
2c: CATH_1b12D01 (D:77-153,D:263-320)
2d: CATH_1b12A01 (A:77-153,A: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 bl21(de3). Organism_taxid: 469008. Strain: bl21(de3).
(1)
1a
1b12A02
A:154-188,A:224-262
1b
1b12C02
C:154-188,C:224-262
1c
1b12B02
B:154-188,B:224-262
1d
1b12D02
D:154-188,D:224-262
Architecture
:
Ribbon
(789)
Topology
:
Umud Fragment, subunit A
(13)
Homologous Superfamily
:
Umud Fragment, subunit A
(13)
Escherichia coli bl21(de3). Organism_taxid: 469008. Strain: bl21(de3).
(1)
2a
1b12B01
B:79-153,B:263-319
2b
1b12C01
C:78-153,C:263-321
2c
1b12D01
D:77-153,D:263-320
2d
1b12A01
A:77-153,A:263-323
[
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
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 (162 KB)
Header - Asym.Unit
Biol.Unit 1 (44 KB)
Header - Biol.Unit 1
Biol.Unit 2 (40 KB)
Header - Biol.Unit 2
Biol.Unit 3 (42 KB)
Header - Biol.Unit 3
Biol.Unit 4 (41 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
1B12
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help