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.
3RMZ
Asym. Unit
Info
Asym.Unit (600 KB)
Biol.Unit 1 (588 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 W199F-MAUG/PRE-METHYLAMINE DEHYDROGENASE COMPLEX
Authors
:
L. M. R. Jensen, C. M. Wilmot
Date
:
21 Apr 11 (Deposition) - 05 Oct 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Maug, Methylamine Dehydrogenase, C-Heme, Quinone Cofactor, Electron Transport, Oxidoreductase-Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. A. Tarboush, L. M. Jensen, E. T. Yukl, J. Geng, A. Liu, C. M. Wilmot, V. L. Davidson
Mutagenesis Of Tryptophan199 Suggests That Hopping Is Required For Maug-Dependent Tryptophan Tryptophylquinone Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 108 16956 2011
[
close entry info
]
Hetero Components
(10, 19)
Info
All Hetero Components
01a: 7-HYDROXY-L-TRYPTOPHAN (0AFa)
01b: 7-HYDROXY-L-TRYPTOPHAN (0AFb)
02a: ACETATE ION (ACTa)
03a: CALCIUM ION (CAa)
03b: CALCIUM ION (CAb)
04a: 1,2-ETHANEDIOL (EDOa)
04b: 1,2-ETHANEDIOL (EDOb)
05a: HEME C (HECa)
05b: HEME C (HECb)
05c: HEME C (HECc)
05d: HEME C (HECd)
06a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
07a: SODIUM ION (NAa)
07b: SODIUM ION (NAb)
07c: SODIUM ION (NAc)
07d: SODIUM ION (NAd)
08a: HEXAETHYLENE GLYCOL (P6Ga)
09a: DI(HYDROXYETHYL)ETHER (PEGa)
10a: TETRAETHYLENE GLYCOL (PG4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0AF
2
Mod. Amino Acid
7-HYDROXY-L-TRYPTOPHAN
2
ACT
1
Ligand/Ion
ACETATE ION
3
CA
2
Ligand/Ion
CALCIUM ION
4
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
5
HEC
4
Ligand/Ion
HEME C
6
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7
NA
4
Ligand/Ion
SODIUM ION
8
P6G
1
Ligand/Ion
HEXAETHYLENE GLYCOL
9
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
10
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:66 , THR A:275 , PRO A:277 , HOH A:378 , HOH A:380 , HOH A:387 , HOH A:396
BINDING SITE FOR RESIDUE CA A 400
02
AC2
SOFTWARE
ASN A:231 , THR A:233 , HOH A:382 , HOH A:492 , HOH A:854 , HOH A:934
BINDING SITE FOR RESIDUE NA A 401
03
AC3
SOFTWARE
LEU A:250 , ARG A:252 , ILE A:255 , HOH A:777 , HOH A:947 , HOH A:1611
BINDING SITE FOR RESIDUE NA A 402
04
AC4
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 , GLU A:113 , MET A:114 , GLN A:163 , LYS A:265 , HOH A:444 , HOH A:530 , HOH A:1195 , HOH A:1350 , HOH A:1962 , HOH A:1966
BINDING SITE FOR RESIDUE HEC A 500
05
AC5
SOFTWARE
TRP A:93 , ASN A:200 , CYS A:201 , CYS A:204 , HIS A:205 , HIS A:224 , LEU A:228 , PHE A:264 , PRO A:267 , LEU A:269 , 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:426 , HOH A:442 , HOH A:456
BINDING SITE FOR RESIDUE HEC A 600
06
AC6
SOFTWARE
ASN B:66 , THR B:275 , PRO B:277 , HOH B:383 , HOH B:399 , HOH B:417 , HOH B:443
BINDING SITE FOR RESIDUE CA B 400
07
AC7
SOFTWARE
ASN B:231 , THR B:233 , HOH B:411 , HOH B:999 , HOH B:1109 , HOH B:1146
BINDING SITE FOR RESIDUE NA B 401
08
AC8
SOFTWARE
LEU B:250 , ARG B:252 , ILE B:255 , HOH B:517 , HOH B:818 , HOH B:1261
BINDING SITE FOR RESIDUE NA B 402
09
AC9
SOFTWARE
GLN B:29 , SER B:30 , CYS B:31 , CYS B:34 , HIS B:35 , 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 , ALA B:104 , PRO B:107 , MET B:114 , GLN B:163 , LYS B:265 , HOH B:549 , HOH B:605 , HOH B:770 , HOH B:901 , HOH B:1931
BINDING SITE FOR RESIDUE HEC B 500
10
BC1
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 , SER B:324 , GLU B:327 , HOH B:375 , HOH B:399 , HOH B:417 , HOH B:423 , HOH B:430
BINDING SITE FOR RESIDUE HEC B 600
11
BC2
SOFTWARE
THR F:187 , LYS F:236 , LEU F:254 , SER F:255 , SER F:256 , GLY F:257 , HOH F:851 , HOH F:990
BINDING SITE FOR RESIDUE PG4 F 387
12
BC3
SOFTWARE
ARG A:25 , ARG A:125 , ASP A:128 , GLU F:218 , VAL F:219 , PHE F:261 , HOH F:903 , HOH F:1748
BINDING SITE FOR RESIDUE P6G F 388
13
BC4
SOFTWARE
ALA A:164 , ARG A:215
BINDING SITE FOR RESIDUE EDO A 374
14
BC5
SOFTWARE
ALA B:164 , ARG B:215
BINDING SITE FOR RESIDUE EDO B 374
15
BC6
SOFTWARE
THR D:187 , GLN D:235 , LYS D:236 , ALA D:237 , GLY D:238 , LEU D:254 , SER D:255 , HOH D:1956
BINDING SITE FOR RESIDUE PEG D 387
16
BC7
SOFTWARE
GLU B:137 , ALA B:138 , LEU B:139 , PHE B:140 , GLY B:141 , ARG F:35 , LEU F:37 , GLU F:38 , HOH F:502 , HOH F:1843
BINDING SITE FOR RESIDUE MES F 389
17
BC8
SOFTWARE
ARG D:35 , LEU D:37 , GLU D:38 , HOH D:477 , HOH D:1158
BINDING SITE FOR RESIDUE ACT D 388
[
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_d3rmzd_ (D:)
1b: SCOP_d3rmzf_ (F:)
2a: SCOP_d3rmzc_ (C:)
2b: SCOP_d3rmze_ (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
d3rmzd_
D:
1b
d3rmzf_
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
d3rmzc_
C:
2b
d3rmze_
E:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (600 KB)
Header - Asym.Unit
Biol.Unit 1 (588 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
3RMZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help