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.
1H4J
Biol. Unit 1
Info
Asym.Unit (420 KB)
Biol.Unit 1 (211 KB)
Biol.Unit 2 (211 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
METHYLOBACTERIUM EXTORQUENS METHANOL DEHYDROGENASE D303E MUTANT
Authors
:
F. Mohammed, R. Gill, D. Thompson, J. B. Cooper, S. P. Wood, P. R. Afolabi, C. Anthony
Date
:
11 May 01 (Deposition) - 23 Aug 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Oxidoreductase, Dehydrogenase, Quinoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. R. Afolabi, F. Mohammed, K. Amaratunga, O. Majekodunmi, S. L. Dales, R. Gill, D. Thompson, J. B. Cooper, S. P. Wood, P. M. Goodwin, C. Anthony
Site-Directed Mutagenesis And X-Ray Crystallography Of The Pqq-Containing Quinoprotein Methanol Dehydrogenase And Its Electron Acceptor, Cytochrome C(L)(, )
Biochemistry V. 40 9799 2001
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: PYRROLOQUINOLINE QUINONE (PQQa)
2b: PYRROLOQUINOLINE QUINONE (PQQb)
2c: PYRROLOQUINOLINE QUINONE (PQQc)
2d: PYRROLOQUINOLINE QUINONE (PQQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
PQQ
2
Ligand/Ion
PYRROLOQUINOLINE QUINONE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:177 , ASN A:261 , GLU A:303 , PQQ A:601
BINDING SITE FOR RESIDUE CA A 701
2
AC2
SOFTWARE
GLU C:177 , ASN C:261 , GLU C:303 , PQQ C:601
BINDING SITE FOR RESIDUE CA C 701
3
AC5
SOFTWARE
GLU A:55 , CYS A:104 , VAL A:107 , ARG A:109 , THR A:159 , SER A:174 , GLY A:175 , ALA A:176 , GLU A:177 , THR A:241 , TRP A:243 , ASN A:261 , GLU A:303 , ARG A:331 , ASN A:394 , TRP A:476 , GLY A:539 , TRP A:540 , CA A:701
BINDING SITE FOR RESIDUE PQQ A 601
4
AC6
SOFTWARE
GLU C:55 , CYS C:104 , VAL C:107 , ARG C:109 , THR C:159 , SER C:174 , GLY C:175 , ALA C:176 , GLU C:177 , THR C:241 , TRP C:243 , ASN C:261 , GLU C:303 , ARG C:331 , ASN C:394 , TRP C:476 , GLY C:539 , TRP C:540 , CA C:701
BINDING SITE FOR RESIDUE PQQ C 601
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: BACTERIAL_PQQ_1 (A:13-41,C:13-41)
2: BACTERIAL_PQQ_2 (A:243-264,C:243-264)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIAL_PQQ_1
PS00363
Bacterial quinoprotein dehydrogenases signature 1.
DHM1_METEA
40-68
2
A:13-41
C:13-41
-
-
2
BACTERIAL_PQQ_2
PS00364
Bacterial quinoprotein dehydrogenases signature 2.
DHM1_METEA
270-291
2
A:243-264
C:243-264
-
-
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1h4jb_ (B:)
1b: SCOP_d1h4jd_ (D:)
1c: SCOP_d1h4jf_ (F:)
1d: SCOP_d1h4jh_ (H:)
2a: SCOP_d1h4ja_ (A:)
2b: SCOP_d1h4jc_ (C:)
2c: SCOP_d1h4je_ (E:)
2d: SCOP_d1h4jg_ (G:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Non-globular all-alpha subunits of globular proteins
(135)
Superfamily
:
Methanol dehydrogenase subunit
(10)
Family
:
Methanol dehydrogenase subunit
(10)
Protein domain
:
Methanol dehydrogenase, light chain
(9)
Methylobacterium extorquens [TaxId: 408]
(3)
1a
d1h4jb_
B:
1b
d1h4jd_
D:
1c
d1h4jf_
F:
1d
d1h4jh_
H:
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
Quinoprotein alcohol dehydrogenase-like
(14)
Family
:
Quinoprotein alcohol dehydrogenase-like
(13)
Protein domain
:
Methanol dehydrogenase, heavy chain
(9)
Methylobacterium extorquens [TaxId: 408]
(3)
2a
d1h4ja_
A:
2b
d1h4jc_
C:
2c
d1h4je_
E:
2d
d1h4jg_
G:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1h4jB00 (B:1-72)
1b: CATH_1h4jD00 (D:1-72)
1c: CATH_1h4jF00 (F:1-72)
1d: CATH_1h4jH00 (H:1-72)
2a: CATH_1h4jA00 (A:1-595)
2b: CATH_1h4jC00 (C:1-595)
2c: CATH_1h4jE00 (E:1-595)
2d: CATH_1h4jG00 (G:1-595)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Methanol Dehydrogenase; Chain B
(10)
Homologous Superfamily
:
Methanol Dehydrogenase, chain B
(10)
Methylobacterium extorquens. Organism_taxid: 408.
(3)
1a
1h4jB00
B:1-72
1b
1h4jD00
D:1-72
1c
1h4jF00
F:1-72
1d
1h4jH00
H:1-72
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.10, no name defined]
(14)
Methylobacterium extorquens. Organism_taxid: 408.
(3)
2a
1h4jA00
A:1-595
2b
1h4jC00
C:1-595
2c
1h4jE00
E:1-595
2d
1h4jG00
G:1-595
[
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
Chain B
Chain C
Chain D
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 (420 KB)
Header - Asym.Unit
Biol.Unit 1 (211 KB)
Header - Biol.Unit 1
Biol.Unit 2 (211 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
1H4J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help