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.
1Z42
Biol. Unit 1
Info
Asym.Unit (128 KB)
Biol.Unit 1 (239 KB)
Biol.Unit 2 (121 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 OXIDIZED YQJM FROM BACILLUS SUBTILIS COMPLEXED WITH P-HYDROXYBENZALDEHYDE
Authors
:
K. Kitzing, T. B. Fitzpatrick, C. Wilken, J. Sawa, G. P. Bourenkov, P. Ma T. Clausen
Date
:
15 Mar 05 (Deposition) - 17 May 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Biol. Unit 2: A,B (1x)
Keywords
:
Flavin, Fmn, P-Hydroxybenzaldehyde, Beta-Alpha-Barrel, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Kitzing, T. B. Fitzpatrick, C. Wilken, J. Sawa, G. P. Bourenkov, P. Macheroux, T. Clausen
The 1. 3 A Crystal Structure Of The Flavoprotein Yqjm Reveal A Novel Class Of Old Yellow Enzymes
J. Biol. Chem. V. 280 27904 2005
[
close entry info
]
Hetero Components
(4, 52)
Info
All Hetero Components
1a: FLAVIN MONONUCLEOTIDE (FMNa)
1b: FLAVIN MONONUCLEOTIDE (FMNb)
2a: P-HYDROXYBENZALDEHYDE (HBAa)
2b: P-HYDROXYBENZALDEHYDE (HBAb)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMN
4
Ligand/Ion
FLAVIN MONONUCLEOTIDE
2
HBA
4
Ligand/Ion
P-HYDROXYBENZALDEHYDE
3
MSE
40
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:1703 , ARG B:318 , HOH B:1645 , HOH B:1772
BINDING SITE FOR RESIDUE SO4 B 1504
2
AC2
SOFTWARE
ARG A:318 , LYS A:322 , ARG B:312 , HOH B:1632 , HOH B:1768
BINDING SITE FOR RESIDUE SO4 A 1505
3
AC3
SOFTWARE
SER A:23 , PRO A:24 , MSE A:25 , CYS A:26 , ALA A:60 , GLN A:102 , HIS A:164 , HIS A:167 , ARG A:215 , VAL A:283 , GLY A:284 , MSE A:285 , GLY A:307 , ARG A:308 , HBA A:1502 , HOH A:1508 , HOH A:1516 , HOH A:1517 , HOH A:1532 , HOH A:1595 , ARG B:336
BINDING SITE FOR RESIDUE FMN A 1500
4
AC4
SOFTWARE
SER B:23 , PRO B:24 , MSE B:25 , CYS B:26 , ALA B:60 , GLN B:102 , HIS B:164 , HIS B:167 , ARG B:215 , VAL B:283 , GLY B:284 , MSE B:285 , GLY B:307 , ARG B:308 , HBA B:1503 , HOH B:1508 , HOH B:1519 , HOH B:1527 , HOH B:1548 , HOH B:1569
BINDING SITE FOR RESIDUE FMN B 1501
5
AC5
SOFTWARE
TYR A:28 , HIS A:164 , HIS A:167 , TYR A:169 , FMN A:1500
BINDING SITE FOR RESIDUE HBA A 1502
6
AC6
SOFTWARE
TYR B:28 , ILE B:69 , HIS B:164 , HIS B:167 , TYR B:169 , FMN B:1501 , HOH B:1793
BINDING SITE FOR RESIDUE HBA B 1503
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1z42a_ (A:)
1b: SCOP_d1z42b_ (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
:
FMN-linked oxidoreductases
(290)
Family
:
FMN-linked oxidoreductases
(242)
Protein domain
:
NADPH dehydrogenase NamA
(4)
Bacillus subtilis [TaxId: 1423]
(4)
1a
d1z42a_
A:
1b
d1z42b_
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_Oxidored_FMN_1z42B01 (B:4-327)
1b: PFAM_Oxidored_FMN_1z42B02 (B:4-327)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
Oxidored_FMN
(38)
Bacillus subtilis
(4)
1a
Oxidored_FMN-1z42B01
B:4-327
1b
Oxidored_FMN-1z42B02
B:4-327
[
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
Asymmetric Unit 2
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 (128 KB)
Header - Asym.Unit
Biol.Unit 1 (239 KB)
Header - Biol.Unit 1
Biol.Unit 2 (121 KB)
Header - Biol.Unit 2
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
1Z42
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
