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.
1ZLP
Asym. Unit
Info
Asym.Unit (97 KB)
Biol.Unit 1 (179 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PETAL DEATH PROTEIN PSR132 WITH CYSTEINE-LINKED GLUTARALDEHYDE FORMING A THIOHEMIACETAL ADDUCT
Authors
:
A. Teplyakov, S. Liu, Z. Lu, A. Howard, D. Dunaway-Mariano, O. Herzberg
Date
:
08 May 05 (Deposition) - 03 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Tim-Barrel, Helix Swapping, 2-Ethyl-3-Methylmalate Lyase, 2-Propyl-3- Methylmalate Lyase, Lyase/Pep Mutase Superfamily, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Teplyakov, S. Liu, Z. Lu, A. Howard, D. Dunaway-Mariano, O. Herzber
Crystal Structure Of The Petal Death Protein From Carnation Flower.
Biochemistry V. 44 16377 2005
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: 5-HYDROXYPENTANAL (GAQa)
1b: 5-HYDROXYPENTANAL (GAQb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAQ
2
Ligand/Ion
5-HYDROXYPENTANAL
2
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:79 , ASP A:107 , ASP A:109 , LYS A:142 , GAQ A:402
BINDING SITE FOR RESIDUE MG A 401
2
AC2
SOFTWARE
ASP B:79 , ASP B:107 , LYS B:142 , GAQ B:402
BINDING SITE FOR RESIDUE MG B 401
3
AC3
SOFTWARE
CYS A:144 , GLY A:145 , ARG A:179 , ASN A:231 , ILE A:233 , LEU A:258 , MG A:401
BINDING SITE FOR RESIDUE GAQ A 402
4
AC4
SOFTWARE
TYR B:68 , CYS B:144 , GLY B:145 , ARG B:179 , GLU B:209 , ASN B:231 , ILE B:233 , LEU B:258 , MG B:401
BINDING SITE FOR RESIDUE GAQ B 402
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ISOCITRATE_LYASE (A:142-147,B:142-147)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISOCITRATE_LYASE
PS00161
Isocitrate lyase signature.
PDP_DIACA
142-147
2
A:142-147
B:142-147
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1zlpa_ (A:)
1b: SCOP_d1zlpb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
automated matches
(16)
Protein domain
:
automated matches
(16)
Clove pink (Dianthus caryophyllus) [TaxId: 3570]
(1)
1a
d1zlpa_
A:
1b
d1zlpb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PEP_mutase_1zlpB01 (B:31-276)
1b: PFAM_PEP_mutase_1zlpB02 (B:31-276)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PK_TIM
(63)
Family
:
PEP_mutase
(13)
Dianthus caryophyllus (Carnation) (Clove pink)
(1)
1a
PEP_mutase-1zlpB01
B:31-276
1b
PEP_mutase-1zlpB02
B:31-276
[
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
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 (97 KB)
Header - Asym.Unit
Biol.Unit 1 (179 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
1ZLP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help