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.
3MZO
Biol. Unit 3
Info
Asym.Unit (227 KB)
Biol.Unit 1 (433 KB)
Biol.Unit 2 (153 KB)
Biol.Unit 3 (144 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 HD-DOMAIN PHOSPHOHYDROLASE (LIN2634) FROM LISTERIA INNOCUA AT 1.98 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
12 May 10 (Deposition) - 26 May 10 (Release) - 26 May 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.98
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Biol. Unit 2: A (2x)
Biol. Unit 3: B,C (1x)
Keywords
:
Hd-Domain Phosphohydrolase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Hd-Domain Phosphohydrolase (Lin2634) From Listeria Innocua At 1. 98 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(2, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
3b: DI(HYDROXYETHYL)ETHER (PEGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
MSE
10
Mod. Amino Acid
SELENOMETHIONINE
3
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
7: BC2 (SOFTWARE)
8: BC3 (SOFTWARE)
9: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
ASP A:50 , HOH A:605 , GLU B:54 , HOH B:457 , HOH B:518
BINDING SITE FOR RESIDUE CA A 306
2
AC5
SOFTWARE
HOH A:366 , HOH A:516 , ASP B:50 , HOH B:377 , HOH C:389 , HOH C:560
BINDING SITE FOR RESIDUE CA A 307
3
AC7
SOFTWARE
GLY A:75 , GLY B:75
BINDING SITE FOR RESIDUE PEG A 313
4
AC8
SOFTWARE
HIS B:33 , HIS B:67 , ASP B:68 , ASP B:137 , HOH B:576
BINDING SITE FOR RESIDUE CA B 302
5
AC9
SOFTWARE
HOH B:472 , HOH B:476 , HOH B:592 , HOH B:628
BINDING SITE FOR RESIDUE CA B 309
6
BC1
SOFTWARE
HIS B:67 , ASP B:68 , HOH B:477 , HOH B:550 , HOH B:575 , HOH B:576 , HOH B:686
BINDING SITE FOR RESIDUE CA B 310
7
BC2
SOFTWARE
LYS B:131 , HOH B:646 , HOH B:656 , HOH B:667
BINDING SITE FOR RESIDUE PEG B 312
8
BC3
SOFTWARE
ARG C:18 , HIS C:33 , HIS C:67 , ASP C:68 , ASP C:137
BINDING SITE FOR RESIDUE CA C 303
9
BC4
SOFTWARE
HIS C:67 , ASP C:68 , SER C:70 , GLU C:96 , HOH C:336
BINDING SITE FOR RESIDUE CA C 311
[
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_HD_2_3mzoC01 (C:1-210)
1b: PFAM_HD_2_3mzoC02 (C:1-210)
1c: PFAM_HD_2_3mzoC03 (C:1-210)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
HD_2
(1)
Listeria innocua
(1)
1a
HD_2-3mzoC01
C:1-210
1b
HD_2-3mzoC02
C:1-210
1c
HD_2-3mzoC03
C:1-210
[
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
Chain C
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 (227 KB)
Header - Asym.Unit
Biol.Unit 1 (433 KB)
Header - Biol.Unit 1
Biol.Unit 2 (153 KB)
Header - Biol.Unit 2
Biol.Unit 3 (144 KB)
Header - Biol.Unit 3
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
3MZO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help