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.
3BUL
Asym. Unit
Info
Asym.Unit (103 KB)
Biol.Unit 1 (97 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
E. COLI I690C/G743C METH C-TERMINAL FRAGMENT (649-1227)
Authors
:
M. Koutmos, K. A. Pattridge, M. L. Ludwig
Date
:
03 Jan 08 (Deposition) - 01 Apr 08 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Meth, Transferase, Reactivation Conformation, H759, Cobalamin, Intermodular Interactions, Amino-Acid Biosynthesis, Cobalt, Metal- Binding, Methionine Biosynthesis, Methyltransferase, S-Adenosyl-L- Methionine
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Datta, M. Koutmos, K. A. Pattridge, M. L. Ludwig, R. G. Matthews
A Disulfide-Stabilized Conformer Of Methionine Synthase Reveals An Unexpected Role For The Histidine Ligand Of The Cobalamin Cofactor.
Proc. Natl. Acad. Sci. Usa V. 105 4115 2008
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: COBALAMIN (B12a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B12
1
Ligand/Ion
COBALAMIN
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:759 , GLY A:802 , LEU A:803 , SER A:804 , LEU A:806 , ILE A:807 , THR A:808 , ARG A:823 , GLN A:824 , LEU A:831 , GLY A:833 , GLY A:834 , ALA A:835 , THR A:836 , GLN A:858 , ASN A:859 , ALA A:860 , THR A:863 , MET A:952 , ASP A:1093 , ALA A:1136 , PRO A:1137 , GLY A:1138 , TYR A:1139 , HIS A:1145 , ALA A:1170 , MET A:1171 , PRO A:1173 , GLY A:1174 , SER A:1176 , SER A:1178 , HOH A:1331 , HOH A:1342
BINDING SITE FOR RESIDUE B12 A 1301
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: B12_BINDING (A:746-881)
2: ADOMET_ACTIVATION (A:897-1227)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
B12_BINDING
PS51332
B12-binding domain profile.
METH_ECOLI
746-881
1
A:746-881
2
ADOMET_ACTIVATION
PS50974
AdoMet activation domain profile.
METH_ECOLI
897-1227
1
A:897-1227
[
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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3bula1 (A:651-740)
2a: SCOP_d3bula3 (A:901-1227)
3a: SCOP_d3bula2 (A:741-896)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Methionine synthase domain-like
(29)
Superfamily
:
Methionine synthase domain
(5)
Family
:
Methionine synthase domain
(5)
Protein domain
:
Methionine synthase domain
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d3bula1
A:651-740
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Methionine synthase activation domain-like
(7)
Superfamily
:
Methionine synthase activation domain-like
(7)
Family
:
Methionine synthase SAM-binding domain
(5)
Protein domain
:
Methionine synthase SAM-binding domain
(5)
Escherichia coli [TaxId: 562]
(5)
2a
d3bula3
A:901-1227
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Cobalamin (vitamin B12)-binding domain
(29)
Family
:
Cobalamin (vitamin B12)-binding domain
(29)
Protein domain
:
Methionine synthase, C-terminal domain
(5)
Escherichia coli [TaxId: 562]
(5)
3a
d3bula2
A:741-896
[
close SCOP info
]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_3bulA02 (A:743-895)
2a: CATH_3bulA03 (A:901-935,A:996-1227)
3a: CATH_3bulA04 (A:936-995)
4a: CATH_3bulA01 (A:651-737)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.280, no name defined]
(23)
Escherichia coli. Organism_taxid: 562.
(4)
1a
3bulA02
A:743-895
Architecture
:
Roll
(3276)
Topology
:
Cobalamin-dependent Methionine Synthase; domain 1
(7)
Homologous Superfamily
:
Cobalamin-dependent Methionine Synthase, domain 1
(7)
Escherichia coli. Organism_taxid: 562.
(4)
2a
3bulA03
A:901-935,A:996-1227
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cobalamin-dependent Methionine Synthase; domain 2
(6)
Homologous Superfamily
:
Cobalamin-dependent Methionine Synthase, domain 2
(6)
Escherichia coli. Organism_taxid: 562.
(4)
3a
3bulA04
A:936-995
Topology
:
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
(21)
Homologous Superfamily
:
Methyltransferase
(6)
Escherichia coli. Organism_taxid: 562.
(4)
4a
3bulA01
A:651-737
[
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
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 (103 KB)
Header - Asym.Unit
Biol.Unit 1 (97 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
3BUL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
