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.
3IML
Biol. Unit 1
Info
Asym.Unit (216 KB)
Biol.Unit 1 (112 KB)
Biol.Unit 2 (102 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 S-ADENOSYLMETHIONINE SYNTHETASE FROM BURKHOLDERIA PSEUDOMALLEI
Authors
:
B. L. Staker
Date
:
10 Aug 09 (Deposition) - 22 Sep 09 (Release) - 30 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
S-Adenosylmethionine Synthetase, Structural Genomics, Atp-Binding, Cobalt, Magnesium, Metal-Binding, Nucleotide-Binding, One-Carbon Metabolism, Potassium, Transferase, Seattle Structural Genomics Center For Infectious Disease, Ssgcid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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: ADOMET_SYNTHASE_1 (A:119-129,B:119-129)
2: ADOMET_SYNTHASE_2 (A:262-270,B:262-270)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADOMET_SYNTHASE_1
PS00376
S-adenosylmethionine synthase signature 1.
METK_BURPS
119-129
2
A:119-129
B:119-129
-
-
2
ADOMET_SYNTHASE_2
PS00377
S-adenosylmethionine synthase signature 2.
METK_BURPS
262-270
2
A:262-270
B:262-270
-
-
[
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, 11)
Info
All SCOP Domains
1a: SCOP_d3imla1 (A:0-102)
1b: SCOP_d3imla2 (A:115-235)
1c: SCOP_d3imld2 (D:123-235)
1d: SCOP_d3imla3 (A:236-388)
1e: SCOP_d3imlb1 (B:5-99)
1f: SCOP_d3imlb2 (B:115-235)
1g: SCOP_d3imlb3 (B:236-387)
1h: SCOP_d3imlc1 (C:4-101)
1i: SCOP_d3imlc2 (C:116-235)
1j: SCOP_d3imlc3 (C:236-378)
1k: SCOP_d3imld1 (D:5-100)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
S-adenosylmethionine synthetase
(23)
Superfamily
:
S-adenosylmethionine synthetase
(23)
Family
:
automated matches
(8)
Protein domain
:
automated matches
(8)
Burkholderia pseudomallei [TaxId: 28450]
(1)
1a
d3imla1
A:0-102
1b
d3imla2
A:115-235
1c
d3imld2
D:123-235
1d
d3imla3
A:236-388
1e
d3imlb1
B:5-99
1f
d3imlb2
B:115-235
1g
d3imlb3
B:236-387
1h
d3imlc1
C:4-101
1i
d3imlc2
C:116-235
1j
d3imlc3
C:236-378
1k
d3imld1
D:5-100
[
close SCOP info
]
CATH Domains
(1, 9)
Info
all CATH domains
1a: CATH_3imlC03 (C:116-139,C:274-378)
1b: CATH_3imlB03 (B:115-139,B:274-387)
1c: CATH_3imlA03 (A:115-139,A:274-388)
1d: CATH_3imlA01 (A:0-11,A:140-236)
1e: CATH_3imlC01 (C:4-11,C:140-236)
1f: CATH_3imlB01 (B:5-11,B:140-236)
1g: CATH_3imlA02 (A:12-102,A:237-273)
1h: CATH_3imlC02 (C:12-101,C:237-273)
1i: CATH_3imlB02 (B:12-99,B:237-273)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GMP Synthetase; Chain A, domain 3
(192)
Homologous Superfamily
:
[code=3.30.300.10, no name defined]
(22)
Pseudomonas pseudomallei (Burkholderia pseudomallei)
(1)
1a
3imlC03
C:116-139,C:274-378
1b
3imlB03
B:115-139,B:274-387
1c
3imlA03
A:115-139,A:274-388
1d
3imlA01
A:0-11,A:140-236
1e
3imlC01
C:4-11,C:140-236
1f
3imlB01
B:5-11,B:140-236
1g
3imlA02
A:12-102,A:237-273
1h
3imlC02
C:12-101,C:237-273
1i
3imlB02
B:12-99,B:237-273
[
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
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 (216 KB)
Header - Asym.Unit
Biol.Unit 1 (112 KB)
Header - Biol.Unit 1
Biol.Unit 2 (102 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
3IML
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help