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.
3L4O
Asym. Unit
Info
Asym.Unit (306 KB)
Biol.Unit 1 (296 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 THE MAUG/PRE-METHYLAMINE DEHYDROGENASE COMPLEX AFTER TREATMENT WITH HYDROGEN PEROXIDE
Authors
:
L. M. R. Jensen, C. M. Wilmot
Date
:
21 Dec 09 (Deposition) - 23 Mar 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Maug, Methylamine Dehydrogenase, Quinone Cofactor, Ttq, His-Tyr Heme, Electron Transport, C-Heme, Iron, Metal-Binding, Oxidoreductase, Transport, Disulfide Bond, Oxidoreductase-Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. M. Jensen, R. Sanishvili, V. L. Davidson, C. M. Wilmot
In Crystallo Posttranslational Modification Within A Maug/Pre-Methylamine Dehydrogenase Complex.
Science V. 327 1392 2010
[
close entry info
]
Hetero Components
(6, 11)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: ACETATE ION (ACTa)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: HEME C (HECa)
4b: HEME C (HECb)
4c: HEME C (HECc)
4d: HEME C (HECd)
5a: TETRAETHYLENE GLYCOL (PG4a)
6a: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQa)
6b: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
ACT
1
Ligand/Ion
ACETATE ION
3
CA
2
Ligand/Ion
CALCIUM ION
4
HEC
4
Ligand/Ion
HEME C
5
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
6
TRQ
2
Mod. Amino Acid
2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:66 , THR A:275 , PRO A:277 , HOH A:379 , HOH A:380 , HOH A:387 , HOH A:397
BINDING SITE FOR RESIDUE CA A 400
2
AC2
SOFTWARE
GLN A:29 , SER A:30 , CYS A:31 , CYS A:34 , HIS A:35 , VAL A:55 , ARG A:65 , THR A:67 , PRO A:68 , LEU A:70 , GLN A:91 , PHE A:92 , TRP A:93 , ARG A:96 , LEU A:100 , GLN A:103 , ALA A:104 , PRO A:107 , GLN A:163 , LYS A:265 , HOH A:442 , HOH A:524 , HOH A:1103 , HOH A:1174
BINDING SITE FOR RESIDUE HEC A 500
3
AC3
SOFTWARE
ASN A:200 , CYS A:201 , CYS A:204 , HIS A:205 , HIS A:224 , ILE A:226 , LEU A:228 , PHE A:264 , PRO A:267 , TYR A:278 , MET A:279 , HIS A:280 , LEU A:287 , TYR A:294 , SER A:324 , GLU A:327 , HOH A:380 , HOH A:387 , HOH A:424 , HOH A:440 , HOH A:453
BINDING SITE FOR RESIDUE HEC A 600
4
AC4
SOFTWARE
ASN B:66 , THR B:275 , PRO B:277 , HOH B:383 , HOH B:398 , HOH B:415 , HOH B:440
BINDING SITE FOR RESIDUE CA B 400
5
AC5
SOFTWARE
GLN B:29 , SER B:30 , CYS B:31 , CYS B:34 , HIS B:35 , SER B:54 , VAL B:55 , ARG B:65 , THR B:67 , PRO B:68 , LEU B:70 , GLN B:91 , PHE B:92 , TRP B:93 , ARG B:96 , LEU B:100 , GLN B:103 , PRO B:107 , GLN B:163 , LYS B:265 , HOH B:543 , HOH B:597 , HOH B:750 , HOH B:867
BINDING SITE FOR RESIDUE HEC B 500
6
AC6
SOFTWARE
TRP B:93 , ASN B:200 , CYS B:201 , CYS B:204 , HIS B:205 , HIS B:224 , LEU B:228 , PHE B:264 , PRO B:267 , LEU B:269 , TYR B:278 , MET B:279 , HIS B:280 , LEU B:287 , TYR B:294 , HOH B:374 , HOH B:398 , HOH B:415 , HOH B:421 , HOH B:428
BINDING SITE FOR RESIDUE HEC B 600
7
AC7
SOFTWARE
ARG A:125 , ASP A:128 , PHE F:261 , HOH F:869
BINDING SITE FOR RESIDUE 1PE F 387
8
AC8
SOFTWARE
THR F:187 , LYS F:236 , LEU F:254 , SER F:255
BINDING SITE FOR RESIDUE PG4 F 388
9
AC9
SOFTWARE
ARG F:35 , LEU F:37 , GLU F:38 , HOH F:499
BINDING SITE FOR RESIDUE ACT F 389
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: CYTC (A:9-130,B:9-130|A:176-350,B:176-35...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
MAUG_PARDP
29-150
196-370
4
A:9-130
B:9-130
A:176-350
B:176-350
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d3l4od_ (D:)
1b: SCOP_d3l4of_ (F:)
2a: SCOP_d3l4oc_ (C:)
2b: SCOP_d3l4oe_ (E:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(31)
Family
:
automated matches
(18)
Protein domain
:
automated matches
(18)
Paracoccus denitrificans [TaxId: 318586]
(18)
1a
d3l4od_
D:
1b
d3l4of_
F:
Class
:
Small proteins
(3458)
Fold
:
Methylamine dehydrogenase, L chain
(68)
Superfamily
:
Methylamine dehydrogenase, L chain
(68)
Family
:
Methylamine dehydrogenase, L chain
(41)
Protein domain
:
automated matches
(32)
Paracoccus denitrificans [TaxId: 318586]
(19)
2a
d3l4oc_
C:
2b
d3l4oe_
E:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3l4oD00 (D:11-386)
1b: CATH_3l4oF00 (F:11-386)
2a: CATH_3l4oC00 (C:7-131)
2b: CATH_3l4oE00 (E:7-131)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
7 Propellor
(136)
Topology
:
Methylamine Dehydrogenase; Chain H
(136)
Homologous Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(76)
Paracoccus denitrificans. Organism_taxid: 318586. Strain: pd 1222.
(2)
1a
3l4oD00
D:11-386
1b
3l4oF00
F:11-386
Architecture
:
Sandwich
(5577)
Topology
:
Electron Transport Ethylamine Dehydrogenase
(43)
Homologous Superfamily
:
Electron Transport Ethylamine Dehydrogenase
(43)
Paracoccus denitrificans. Organism_taxid: 318586. Strain: pd 1222.
(2)
2a
3l4oC00
C:7-131
2b
3l4oE00
E:7-131
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Me_amine_dh_H_3l4oF01 (F:43-384)
1b: PFAM_Me_amine_dh_H_3l4oF02 (F:43-384)
2a: PFAM_CCP_MauG_3l4oB01 (B:7-186)
2b: PFAM_CCP_MauG_3l4oB02 (B:7-186)
3a: PFAM_Me_amine_dh_L_3l4oE01 (E:8-130)
3b: PFAM_Me_amine_dh_L_3l4oE02 (E:8-130)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
Me-amine-dh_H
(13)
Paracoccus denitrificans (strain Pd 1222)
(6)
1a
Me-amine-dh_H-3l4oF01
F:43-384
1b
Me-amine-dh_H-3l4oF02
F:43-384
Clan
:
Cytochrome-c
(108)
Family
:
CCP_MauG
(10)
Paracoccus denitrificans (strain Pd 1222)
(6)
2a
CCP_MauG-3l4oB01
B:7-186
2b
CCP_MauG-3l4oB02
B:7-186
Clan
:
no clan defined [family: Me-amine-dh_L]
(16)
Family
:
Me-amine-dh_L
(16)
Paracoccus denitrificans (strain Pd 1222)
(2)
3a
Me-amine-dh_L-3l4oE01
E:8-130
3b
Me-amine-dh_L-3l4oE02
E:8-130
[
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
Chain E
Chain F
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 (306 KB)
Header - Asym.Unit
Biol.Unit 1 (296 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
3L4O
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help