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.
1U6J
Asym. Unit
Info
Asym.Unit (544 KB)
Biol.Unit 1 (271 KB)
Biol.Unit 2 (272 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE OF NATIVE COENZYME F420-DEPENDENT METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE AT 2.4A RESOLUTION
Authors
:
E. Warkentin, C. H. Hagemeier, S. Shima, R. K. Thauer, U. Ermler
Date
:
30 Jul 04 (Deposition) - 01 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Monomer: Alpha/Beta Domain, Helix Bundle; Trimer Of Dimers, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Warkentin, C. H. Hagemeier, S. Shima, R. K. Thauer, U. Ermler
The Structure Of F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase: A Crystallographic 'Superstructure' Of The Selenomethionine-Labelled Protein Crystal Structure.
Acta Crystallogr. , Sect. D V. 61 198 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(8, 8)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:9008 , HOH A:9010 , HOH A:9011 , HOH A:9013 , HOH A:9014 , ASP L:226
BINDING SITE FOR RESIDUE MG A 6001
2
AC2
SOFTWARE
HOH A:8387 , HOH A:9087 , HOH A:9088 , HOH A:9089 , HOH A:9090 , HOH A:9091
BINDING SITE FOR RESIDUE MG A 6002
3
AC3
SOFTWARE
HOH B:9009 , HOH B:9015 , HOH B:9017 , HOH B:9018 , HOH B:9019 , ASP C:226
BINDING SITE FOR RESIDUE MG B 6003
4
AC4
SOFTWARE
GLU B:175 , HOH B:8239 , HOH B:9092 , ARG C:229 , HOH C:8238
BINDING SITE FOR RESIDUE MG B 6004
5
AC5
SOFTWARE
HOH G:8421 , HOH G:9020 , HOH G:9021 , HOH G:9023 , HOH G:9024 , HOH G:9025
BINDING SITE FOR RESIDUE MG G 6005
6
AC6
SOFTWARE
GLU G:91 , HOH G:8021 , HOH G:8235 , HOH G:8236 , HOH G:8243
BINDING SITE FOR RESIDUE MG G 6006
7
AC7
SOFTWARE
GLU H:175 , HOH H:9028 , HOH H:9029 , HOH H:9030 , ARG I:229 , HOH I:8261
BINDING SITE FOR RESIDUE MG H 6007
8
AC8
SOFTWARE
HOH H:8240 , HOH H:9102 , HOH H:9104 , HOH H:9105 , ASP I:226
BINDING SITE FOR RESIDUE MG H 6008
[
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
(0, 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.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1u6ja_ (A:)
1b: SCOP_d1u6jb_ (B:)
1c: SCOP_d1u6jc_ (C:)
1d: SCOP_d1u6jd_ (D:)
1e: SCOP_d1u6je_ (E:)
1f: SCOP_d1u6jf_ (F:)
1g: SCOP_d1u6jg_ (G:)
1h: SCOP_d1u6jh_ (H:)
1i: SCOP_d1u6ji_ (I:)
1j: SCOP_d1u6jj_ (J:)
1k: SCOP_d1u6jk_ (K:)
1l: SCOP_d1u6jl_ (L:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
(7)
Superfamily
:
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
(7)
Family
:
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
(7)
Protein domain
:
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
(7)
Methanopyrus kandleri [TaxId: 2320]
(7)
1a
d1u6ja_
A:
1b
d1u6jb_
B:
1c
d1u6jc_
C:
1d
d1u6jd_
D:
1e
d1u6je_
E:
1f
d1u6jf_
F:
1g
d1u6jg_
G:
1h
d1u6jh_
H:
1i
d1u6ji_
I:
1j
d1u6jj_
J:
1k
d1u6jk_
K:
1l
d1u6jl_
L:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_MTD_1u6jL01 (L:3-282)
1b: PFAM_MTD_1u6jL02 (L:3-282)
1c: PFAM_MTD_1u6jL03 (L:3-282)
1d: PFAM_MTD_1u6jL04 (L:3-282)
1e: PFAM_MTD_1u6jL05 (L:3-282)
1f: PFAM_MTD_1u6jL06 (L:3-282)
1g: PFAM_MTD_1u6jL07 (L:3-282)
1h: PFAM_MTD_1u6jL08 (L:3-282)
1i: PFAM_MTD_1u6jL09 (L:3-282)
1j: PFAM_MTD_1u6jL10 (L:3-282)
1k: PFAM_MTD_1u6jL11 (L:3-282)
1l: PFAM_MTD_1u6jL12 (L:3-282)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: MTD]
(4)
Family
:
MTD
(4)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
(4)
1a
MTD-1u6jL01
L:3-282
1b
MTD-1u6jL02
L:3-282
1c
MTD-1u6jL03
L:3-282
1d
MTD-1u6jL04
L:3-282
1e
MTD-1u6jL05
L:3-282
1f
MTD-1u6jL06
L:3-282
1g
MTD-1u6jL07
L:3-282
1h
MTD-1u6jL08
L:3-282
1i
MTD-1u6jL09
L:3-282
1j
MTD-1u6jL10
L:3-282
1k
MTD-1u6jL11
L:3-282
1l
MTD-1u6jL12
L:3-282
[
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
Chain I
Chain J
Chain K
Chain L
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 (544 KB)
Header - Asym.Unit
Biol.Unit 1 (271 KB)
Header - Biol.Unit 1
Biol.Unit 2 (272 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
1U6J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
