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.
1NVJ
Biol. Unit 1
Info
Asym.Unit (264 KB)
Biol.Unit 1 (86 KB)
Biol.Unit 2 (93 KB)
Biol.Unit 3 (83 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DELETION MUTANT (DELTA 141) OF MOLYBDOPTERIN SYNTHASE
Authors
:
M. J. Rudolph, M. M. Wuebbens, O. Turque, K. V. Rajagopalan, H. Schindel
Date
:
03 Feb 03 (Deposition) - 06 May 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Deletion Mutant, Molybdenum Cofactor Biosynthesis, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Rudolph, M. M. Wuebbens, O. Turque, K. V. Rajagopalan, H. Schindelin
Structural Studies Of Molybdopterin Synthase Provide Insights Into Its Catalytic Mechanism
J. Biol. Chem. V. 278 14514 2003
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
1b: FORMIC ACID (FMTb)
1c: FORMIC ACID (FMTc)
1d: FORMIC ACID (FMTd)
1e: FORMIC ACID (FMTe)
1f: FORMIC ACID (FMTf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
2
Ligand/Ion
FORMIC ACID
2
GOL
4
Ligand/Ion
GLYCEROL
3
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
6: BC2 (SOFTWARE)
7: BC3 (SOFTWARE)
8: BC5 (SOFTWARE)
9: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
HOH A:161 , HOH A:175 , HOH A:176 , GLY B:91 , HOH B:169
BINDING SITE FOR RESIDUE NA B 141
2
AC4
SOFTWARE
HOH A:193 , HOH E:154 , GLY F:91 , HOH F:168 , HOH F:183
BINDING SITE FOR RESIDUE NA F 141
3
AC5
SOFTWARE
SER A:105 , PHE A:108 , GLN B:112 , ASP B:116 , HOH B:147 , ARG C:73 , TRP C:74
BINDING SITE FOR RESIDUE GOL B 142
4
AC7
SOFTWARE
ARG A:39 , HIS B:103 , ARG B:104 , SER B:105
BINDING SITE FOR RESIDUE GOL B 143
5
AC8
SOFTWARE
GLU A:27 , ASP A:28 , PRO A:75 , SER A:101 , ALA A:102
BINDING SITE FOR RESIDUE GOL A 141
6
BC2
SOFTWARE
GLU A:24 , ARG A:78 , PRO E:20 , GLU E:24
BINDING SITE FOR RESIDUE GOL A 142
7
BC3
SOFTWARE
VAL B:7 , TYR D:55 , TRP D:125 , TRP D:136 , VAL D:137
BINDING SITE FOR RESIDUE GOL D 145
8
BC5
SOFTWARE
ARG A:104 , HOH A:155 , PHE B:34 , GLY B:36 , ARG B:39
BINDING SITE FOR RESIDUE FMT A 143
9
BC8
SOFTWARE
HIS B:83 , LYS B:119 , PHE B:124
BINDING SITE FOR RESIDUE FMT B 144
[
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
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1nvja_ (A:)
1b: SCOP_d1nvjb_ (B:)
1c: SCOP_d1nvjc_ (C:)
1d: SCOP_d1nvjd_ (D:)
1e: SCOP_d1nvje_ (E:)
1f: SCOP_d1nvjf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
Molybdopterin synthase subunit MoaE
(10)
Family
:
Molybdopterin synthase subunit MoaE
(5)
Protein domain
:
Molybdopterin synthase subunit MoaE
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d1nvja_
A:
1b
d1nvjb_
B:
1c
d1nvjc_
C:
1d
d1nvjd_
D:
1e
d1nvje_
E:
1f
d1nvjf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1nvjB00 (B:2-127)
1b: CATH_1nvjD00 (D:2-140)
1c: CATH_1nvjC00 (C:2-128)
1d: CATH_1nvjF00 (F:2-127)
1e: CATH_1nvjA00 (A:2-127)
1f: CATH_1nvjE00 (E:2-126)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.40, no name defined]
(6)
Escherichia coli. Organism_taxid: 562.
(3)
1a
1nvjB00
B:2-127
1b
1nvjD00
D:2-140
1c
1nvjC00
C:2-128
1d
1nvjF00
F:2-127
1e
1nvjA00
A:2-127
1f
1nvjE00
E:2-126
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_MoaE_1nvjF01 (F:5-122)
1b: PFAM_MoaE_1nvjF02 (F:5-122)
1c: PFAM_MoaE_1nvjF03 (F:5-122)
1d: PFAM_MoaE_1nvjF04 (F:5-122)
1e: PFAM_MoaE_1nvjF05 (F:5-122)
1f: PFAM_MoaE_1nvjF06 (F:5-122)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: MoaE]
(7)
Family
:
MoaE
(7)
Escherichia coli (strain K12)
(2)
1a
MoaE-1nvjF01
F:5-122
1b
MoaE-1nvjF02
F:5-122
1c
MoaE-1nvjF03
F:5-122
1d
MoaE-1nvjF04
F:5-122
1e
MoaE-1nvjF05
F:5-122
1f
MoaE-1nvjF06
F:5-122
[
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
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 (264 KB)
Header - Asym.Unit
Biol.Unit 1 (86 KB)
Header - Biol.Unit 1
Biol.Unit 2 (93 KB)
Header - Biol.Unit 2
Biol.Unit 3 (83 KB)
Header - Biol.Unit 3
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
1NVJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
