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.
1YLH
Asym. Unit
Info
Asym.Unit (92 KB)
Biol.Unit 1 (87 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 PHOSPHOENOLPYRUVATE CARBOXYKINASE FROM ACTINOBACCILUS SUCCINOGENES IN COMPLEX WITH MANGANESE AND PYRUVATE
Authors
:
Y. A. Leduc, L. Prasad, M. Laivenieks, J. G. Zeikus, L. T. Delbaere
Date
:
19 Jan 05 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Phosphoenolpyruvate Carboxykinase, Disulphide Bond, Bound Sulfhydrl Reducing Agent, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. A. Leduc, L. Prasad, M. Laivenieks, J. G. Zeikus, L. T. Delbaere
Structure Of Pep Carboxykinase From The Succinate-Producing Actinobacillus Succinogenes: A New Conserved Active-Site Motif.
Acta Crystallogr. , Sect. D V. 61 903 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 10)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
2a: (2S,3S)-2,3-DIHYDROXY-4-SULFANYLBU... (DT3a)
3a: FORMIC ACID (FMTa)
3b: FORMIC ACID (FMTb)
3c: FORMIC ACID (FMTc)
4a: MANGANESE (II) ION (MNa)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
6a: PYRUVIC ACID (PYRa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
2
Ligand/Ion
BETA-MERCAPTOETHANOL
2
DT3
1
Ligand/Ion
(2S,3S)-2,3-DIHYDROXY-4-SULFANYLBUTANE-1-SULFONATE
3
FMT
3
Ligand/Ion
FORMIC ACID
4
MN
1
Ligand/Ion
MANGANESE (II) ION
5
PO4
2
Ligand/Ion
PHOSPHATE ION
6
PYR
1
Ligand/Ion
PYRUVIC ACID
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:213 , HIS A:232 , ASP A:269 , HOH A:753 , HOH A:863 , HOH A:864
BINDING SITE FOR RESIDUE MN A 560
02
AC2
SOFTWARE
LEU A:249 , SER A:250 , GLY A:251 , THR A:252 , GLY A:253 , LYS A:254 , THR A:255 , HOH A:818
BINDING SITE FOR RESIDUE PO4 A 921
03
AC3
SOFTWARE
ARG A:154 , TYR A:339 , ARG A:346 , HOH A:656
BINDING SITE FOR RESIDUE PO4 A 922
04
AC4
SOFTWARE
LEU A:108 , LYS A:111 , GLN A:112 , CYS A:175 , THR A:176
BINDING SITE FOR RESIDUE DT3 A 592
05
AC5
SOFTWARE
CYS A:74 , LYS A:79 , TRP A:84
BINDING SITE FOR RESIDUE BME A 593
06
AC6
SOFTWARE
LEU A:265 , ASP A:268 , CYS A:285 , TYR A:336 , HOH A:872
BINDING SITE FOR RESIDUE BME A 594
07
AC7
SOFTWARE
ARG A:65 , TYR A:207 , LYS A:213 , ARG A:333 , PHE A:413 , HOH A:753 , HOH A:857 , HOH A:864
BINDING SITE FOR RESIDUE PYR A 931
08
AC8
SOFTWARE
ALA A:56 , ASP A:58 , LYS A:328 , HOH A:657 , HOH A:694
BINDING SITE FOR RESIDUE FMT A 900
09
AC9
SOFTWARE
PHE A:44 , ASP A:58 , GLY A:60 , THR A:63 , ASN A:312
BINDING SITE FOR RESIDUE FMT A 901
10
BC1
SOFTWARE
PHE A:44 , GLY A:60 , ILE A:61 , GLY A:204 , TRP A:206 , HOH A:613
BINDING SITE FOR RESIDUE FMT A 902
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: PEPCK_ATP (A:265-280)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPCK_ATP
PS00532
Phosphoenolpyruvate carboxykinase (ATP) signature.
PCKA_ACTSZ
263-278
1
A:265-280
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ylha1 (A:4-227)
2a: SCOP_d1ylha2 (A:228-539)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PEP carboxykinase N-terminal domain
(54)
Superfamily
:
PEP carboxykinase N-terminal domain
(54)
Family
:
PEP carboxykinase N-terminal domain
(48)
Protein domain
:
Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
(16)
Actinobacillus succinogenes [TaxId: 67854]
(2)
1a
d1ylha1
A:4-227
Fold
:
PEP carboxykinase-like
(61)
Superfamily
:
PEP carboxykinase-like
(61)
Family
:
PEP carboxykinase C-terminal domain
(48)
Protein domain
:
Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
(16)
Actinobacillus succinogenes [TaxId: 67854]
(2)
2a
d1ylha2
A:228-539
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1ylhA01 (A:4-42,A:67-227)
2a: CATH_1ylhA03 (A:228-283,A:344-539)
3a: CATH_1ylhA02 (A:43-63,A:284-341)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 1
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 1
(42)
Actinobacillus succinogenes. Organism_taxid: 67854.
(2)
1a
1ylhA01
A:4-42,A:67-227
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 3
(62)
Homologous Superfamily
:
[code=3.90.228.20, no name defined]
(42)
Actinobacillus succinogenes. Organism_taxid: 67854.
(2)
2a
1ylhA03
A:228-283,A:344-539
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 2
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 2
(42)
Actinobacillus succinogenes. Organism_taxid: 67854.
(2)
3a
1ylhA02
A:43-63,A:284-341
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PEPCK_ATP_1ylhA01 (A:19-493)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PEP-carboxyk
(36)
Family
:
PEPCK_ATP
(11)
Actinobacillus succinogenes (strain ATCC 55618 / 130Z)
(2)
1a
PEPCK_ATP-1ylhA01
A:19-493
[
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 (92 KB)
Header - Asym.Unit
Biol.Unit 1 (87 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
1YLH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help