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.
1MG2
Biol. Unit 1
Info
Asym.Unit (521 KB)
Biol.Unit 1 (259 KB)
Biol.Unit 2 (262 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN
Authors
:
D. Sun, Z. W. Chen, F. S. Mathews, V. L. Davidson
Date
:
14 Aug 02 (Deposition) - 11 Dec 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: I,J,K,L,M,N,O,P (1x)
Keywords
:
Electron Transfer, Methylamine Dehydrogenase, Cytochrome, Blue Copper Protein, Active Site Mutant, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Sun, Z. W. Chen, F. S. Mathews, V. L. Davidson
Mutation Of Alpha Phe55 Of Methylamine Dehydrogenase Alters The Reorganization Energy And Electronic Coupling For Its Electron Transfer Reaction With Amicyanin
Biochemistry V. 41 13926 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
4e: PHOSPHATE ION (PO4e)
4f: PHOSPHATE ION (PO4f)
4g: PHOSPHATE ION (PO4g)
4h: PHOSPHATE ION (PO4h)
5a: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQa)
5b: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQb)
5c: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQc)
5d: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
-1
Ligand/Ion
COPPER (II) ION
2
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
NA
-1
Ligand/Ion
SODIUM ION
4
PO4
4
Ligand/Ion
PHOSPHATE ION
5
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
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS C:53 , CYS C:92 , HIS C:95 , MET C:98
BINDING SITE FOR RESIDUE CU C 107
02
AC2
SOFTWARE
HIS G:53 , CYS G:92 , HIS G:95 , MET G:98
BINDING SITE FOR RESIDUE CU G 107
03
AC5
SOFTWARE
PHE F:110 , GLY F:111 , ASP F:115 , HOH F:1690 , HOH F:2285 , LYS G:68
BINDING SITE FOR RESIDUE PO4 F 401
04
AC6
SOFTWARE
PHE B:110 , GLY B:111 , ASP B:115 , HOH B:2517 , LYS C:68
BINDING SITE FOR RESIDUE PO4 B 402
05
BC1
SOFTWARE
ALA E:86 , ASP E:87 , ASP E:88 , PRO E:146 , GLY E:148 , HOH E:2614
BINDING SITE FOR RESIDUE PO4 E 406
06
BC2
SOFTWARE
ASP G:18 , ASP M:87 , ASP M:88 , PRO M:146 , GLY M:148 , HOH M:1206
BINDING SITE FOR RESIDUE PO4 M 407
07
BC3
SOFTWARE
ALA A:86 , ASP A:87 , ASP A:88 , PRO A:146
BINDING SITE FOR RESIDUE PO4 A 408
08
BC6
SOFTWARE
GLU G:31 , GLY H:72 , ASP H:75 , TYR H:77 , HOH H:1158
BINDING SITE FOR RESIDUE NA H 603
09
BC7
SOFTWARE
GLU C:31 , GLY D:72 , ASP D:75 , TYR D:77 , HOH D:1002 , HOH D:1409 , HOH D:1768
BINDING SITE FOR RESIDUE NA D 604
10
BC8
SOFTWARE
MET D:56 , CYS D:57 , CYS D:60 , HIS D:61 , PRO D:71 , TRP D:78 , THR D:79 , TYR D:80 , ASN D:83 , LEU D:89 , LEU D:93 , ALA D:97 , THR D:98 , GLN D:100 , MET D:101 , HOH D:1852
BINDING SITE FOR RESIDUE HEM D 200
11
BC9
SOFTWARE
MET H:56 , CYS H:57 , CYS H:60 , HIS H:61 , PRO H:71 , TRP H:78 , THR H:79 , TYR H:80 , ASN H:83 , LEU H:89 , LEU H:93 , ALA H:97 , THR H:98 , GLN H:100 , MET H:101 , HOH H:1646 , HOH H:1903
BINDING SITE FOR RESIDUE HEM H 200
[
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: CYTC (D:30-124,H:30-124)
2: COPPER_BLUE (C:85-98,G:85-98)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
CYCL_PARDE
52-146
2
D:30-124
H:30-124
-
-
2
COPPER_BLUE
PS00196
Type-1 copper (blue) proteins signature.
AMCY_PARDE
111-124
2
C:85-98
G:85-98
-
-
[
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
(4, 16)
Info
All SCOP Domains
1a: SCOP_d1mg2d_ (D:)
1b: SCOP_d1mg2l_ (L:)
1c: SCOP_d1mg2p_ (P:)
1d: SCOP_d1mg2h_ (H:)
2a: SCOP_d1mg2a_ (A:)
2b: SCOP_d1mg2e_ (E:)
2c: SCOP_d1mg2i_ (I:)
2d: SCOP_d1mg2m_ (M:)
3a: SCOP_d1mg2c_ (C:)
3b: SCOP_d1mg2g_ (G:)
3c: SCOP_d1mg2k_ (K:)
3d: SCOP_d1mg2o_ (O:)
4a: SCOP_d1mg2b_ (B:)
4b: SCOP_d1mg2f_ (F:)
4c: SCOP_d1mg2j_ (J:)
4d: SCOP_d1mg2n_ (N:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
monodomain cytochrome c
(197)
Protein domain
:
Cytochrome c551
(13)
Paracoccus denitrificans [TaxId: 266]
(5)
1a
d1mg2d_
D:
1b
d1mg2l_
L:
1c
d1mg2p_
P:
1d
d1mg2h_
H:
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(31)
Family
:
Methylamine dehydrogenase, H-chain
(8)
Protein domain
:
Methylamine dehydrogenase, H-chain
(8)
Paracoccus denitrificans [TaxId: 266]
(5)
2a
d1mg2a_
A:
2b
d1mg2e_
E:
2c
d1mg2i_
I:
2d
d1mg2m_
M:
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Plastocyanin/azurin-like
(241)
Protein domain
:
Amicyanin
(34)
Paracoccus denitrificans [TaxId: 266]
(33)
3a
d1mg2c_
C:
3b
d1mg2g_
G:
3c
d1mg2k_
K:
3d
d1mg2o_
O:
Class
:
Small proteins
(3458)
Fold
:
Methylamine dehydrogenase, L chain
(68)
Superfamily
:
Methylamine dehydrogenase, L chain
(68)
Family
:
Methylamine dehydrogenase, L chain
(41)
Protein domain
:
Methylamine dehydrogenase
(9)
Paracoccus denitrificans [TaxId: 266]
(6)
4a
d1mg2b_
B:
4b
d1mg2f_
F:
4c
d1mg2j_
J:
4d
d1mg2n_
N:
[
close SCOP info
]
CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_1mg2D00 (D:1-147)
1b: CATH_1mg2H00 (H:1-147)
1c: CATH_1mg2L00 (L:1-147)
1d: CATH_1mg2P00 (P:1-147)
2a: CATH_1mg2A00 (A:5-386)
2b: CATH_1mg2E00 (E:5-386)
2c: CATH_1mg2I00 (I:5-386)
2d: CATH_1mg2M00 (M:5-386)
3a: CATH_1mg2B00 (B:7-131)
3b: CATH_1mg2F00 (F:7-131)
3c: CATH_1mg2J00 (J:7-131)
3d: CATH_1mg2N00 (N:7-131)
4a: CATH_1mg2C00 (C:1-105)
4b: CATH_1mg2G00 (G:1-105)
4c: CATH_1mg2K00 (K:1-105)
4d: CATH_1mg2O00 (O:1-105)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Paracoccus denitrificans. Organism_taxid: 266.
(2)
1a
1mg2D00
D:1-147
1b
1mg2H00
H:1-147
1c
1mg2L00
L:1-147
1d
1mg2P00
P:1-147
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: 266.
(3)
2a
1mg2A00
A:5-386
2b
1mg2E00
E:5-386
2c
1mg2I00
I:5-386
2d
1mg2M00
M:5-386
Architecture
:
Sandwich
(5577)
Topology
:
Electron Transport Ethylamine Dehydrogenase
(43)
Homologous Superfamily
:
Electron Transport Ethylamine Dehydrogenase
(43)
Paracoccus denitrificans. Organism_taxid: 266.
(2)
3a
1mg2B00
B:7-131
3b
1mg2F00
F:7-131
3c
1mg2J00
J:7-131
3d
1mg2N00
N:7-131
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
4a
1mg2C00
C:1-105
4b
1mg2G00
G:1-105
4c
1mg2K00
K:1-105
4d
1mg2O00
O:1-105
[
close CATH info
]
Pfam Domains
(4, 16)
Info
all PFAM domains
1a: PFAM_Me_amine_dh_H_1mg2M01 (M:43-384)
1b: PFAM_Me_amine_dh_H_1mg2M02 (M:43-384)
1c: PFAM_Me_amine_dh_H_1mg2M03 (M:43-384)
1d: PFAM_Me_amine_dh_H_1mg2M04 (M:43-384)
2a: PFAM_Copper_bind_1mg2O01 (O:17-105)
2b: PFAM_Copper_bind_1mg2O02 (O:17-105)
2c: PFAM_Copper_bind_1mg2O03 (O:17-105)
2d: PFAM_Copper_bind_1mg2O04 (O:17-105)
3a: PFAM_Cytochrome_CBB3_1mg2P01 (P:45-120)
3b: PFAM_Cytochrome_CBB3_1mg2P02 (P:45-120)
3c: PFAM_Cytochrome_CBB3_1mg2P03 (P:45-120)
3d: PFAM_Cytochrome_CBB3_1mg2P04 (P:45-120)
4a: PFAM_Me_amine_dh_L_1mg2N01 (N:8-130)
4b: PFAM_Me_amine_dh_L_1mg2N02 (N:8-130)
4c: PFAM_Me_amine_dh_L_1mg2N03 (N:8-130)
4d: PFAM_Me_amine_dh_L_1mg2N04 (N:8-130)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
Me-amine-dh_H
(13)
Paracoccus denitrificans
(3)
1a
Me-amine-dh_H-1mg2M01
M:43-384
1b
Me-amine-dh_H-1mg2M02
M:43-384
1c
Me-amine-dh_H-1mg2M03
M:43-384
1d
Me-amine-dh_H-1mg2M04
M:43-384
Clan
:
CU_oxidase
(192)
Family
:
Copper-bind
(82)
Paracoccus denitrificans
(11)
2a
Copper-bind-1mg2O01
O:17-105
2b
Copper-bind-1mg2O02
O:17-105
2c
Copper-bind-1mg2O03
O:17-105
2d
Copper-bind-1mg2O04
O:17-105
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrome_CBB3
(20)
Paracoccus denitrificans
(4)
3a
Cytochrome_CBB3-1mg2P01
P:45-120
3b
Cytochrome_CBB3-1mg2P02
P:45-120
3c
Cytochrome_CBB3-1mg2P03
P:45-120
3d
Cytochrome_CBB3-1mg2P04
P:45-120
Clan
:
no clan defined [family: Me-amine-dh_L]
(16)
Family
:
Me-amine-dh_L
(16)
Paracoccus denitrificans
(7)
4a
Me-amine-dh_L-1mg2N01
N:8-130
4b
Me-amine-dh_L-1mg2N02
N:8-130
4c
Me-amine-dh_L-1mg2N03
N:8-130
4d
Me-amine-dh_L-1mg2N04
N: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
Chain G
Chain H
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 (521 KB)
Header - Asym.Unit
Biol.Unit 1 (259 KB)
Header - Biol.Unit 1
Biol.Unit 2 (262 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
1MG2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help