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.
3M4P
Asym. Unit
Info
Asym.Unit (607 KB)
Biol.Unit 1 (304 KB)
Biol.Unit 2 (301 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ENTAMOEBA HISTOLYTICA ASPARAGINYL-TRNA SYNTHETASE (ASNRS) IN COMPLEX WITH ASPARAGINYL-ADENYLATE
Authors
:
E. T. Larson, E. A. Merritt, Medical Structural Genomics Of Pathogenic Protozoa (Msgpp)
Date
:
11 Mar 10 (Deposition) - 23 Mar 10 (Release) - 23 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.83
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Aminoacyl-Trna Synthetase, Trna Ligase, Aars, Asnrs, Translation, Atp-Binding, Nucleotide-Binding, Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa, Msgpp, Ligase, Protein Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. T. Larson, J. E. Kim, A. Napuli, A. Kelley, L. Castaneda, C. L. M. J. Verlinde, W. C. Van Voorhis, F. S. Buckner, E. Fan, W. G. J. Hol, E. A. Merritt
X-Ray Crystal Structure Of Asparaginyl-Trna Synthetase From The Eukaryotic Human Pathogen Entamoeba Histolytica.
To Be Published
[
close entry info
]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM A... (4ADa)
1b: 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM A... (4ADb)
1c: 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM A... (4ADc)
1d: 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM A... (4ADd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4AD
4
Ligand/Ion
4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'-MONOPHOSPHATE
2
GOL
2
Ligand/Ion
GLYCEROL
3
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
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)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:204 , GLN A:206 , ARG A:227 , GLU A:229 , ARG A:235 , HIS A:236 , LEU A:237 , TYR A:240 , HIS A:242 , GLU A:244 , TYR A:351 , GLU A:374 , ILE A:375 , VAL A:376 , GLY A:377 , ARG A:381 , TYR A:419 , GLY A:420 , GLY A:422 , ARG A:425
BINDING SITE FOR RESIDUE 4AD A 500
02
AC2
SOFTWARE
PRO A:132 , MET A:135 , ARG A:232 , TYR A:445 , ARG A:448
BINDING SITE FOR RESIDUE SO4 A 511
03
AC3
SOFTWARE
ILE A:131 , LYS A:134 , ARG A:437 , LYS A:438
BINDING SITE FOR RESIDUE SO4 A 512
04
AC4
SOFTWARE
TYR A:35 , SER A:144 , GLU A:145 , HIS A:146
BINDING SITE FOR RESIDUE SO4 A 513
05
AC5
SOFTWARE
ARG A:154 , GLU A:239 , TYR A:240 , LEU A:241 , GLU A:424 , CYS A:440 , LEU A:441 , GLN B:174
BINDING SITE FOR RESIDUE GOL A 521
06
AC6
SOFTWARE
SER B:204 , GLN B:206 , ARG B:227 , ARG B:235 , HIS B:236 , LEU B:237 , TYR B:240 , HIS B:242 , GLU B:244 , TYR B:351 , GLU B:374 , ILE B:375 , GLY B:377 , ARG B:381 , TYR B:419 , GLY B:420 , GLY B:422 , ARG B:425
BINDING SITE FOR RESIDUE 4AD B 500
07
AC7
SOFTWARE
ILE B:131 , PRO B:132 , MET B:135 , TYR B:445 , ARG B:448
BINDING SITE FOR RESIDUE SO4 B 511
08
AC8
SOFTWARE
LYS B:134 , ARG B:437 , LYS B:438
BINDING SITE FOR RESIDUE SO4 B 512
09
AC9
SOFTWARE
TYR B:35 , SER B:144 , GLU B:145 , HIS B:146
BINDING SITE FOR RESIDUE SO4 B 513
10
BC1
SOFTWARE
SER C:204 , GLN C:206 , ARG C:227 , GLU C:229 , ARG C:235 , HIS C:236 , LEU C:237 , TYR C:240 , HIS C:242 , GLU C:244 , GLU C:374 , ILE C:375 , VAL C:376 , GLY C:377 , ARG C:381 , TYR C:419 , GLY C:420 , GLY C:422 , ARG C:425 , ILE C:436
BINDING SITE FOR RESIDUE 4AD C 500
11
BC2
SOFTWARE
PRO C:132 , MET C:135 , TYR C:445 , GLU C:447 , ARG C:448
BINDING SITE FOR RESIDUE SO4 C 511
12
BC3
SOFTWARE
LYS C:134 , ARG C:437 , LYS C:438
BINDING SITE FOR RESIDUE SO4 C 512
13
BC4
SOFTWARE
TYR C:35 , SER C:144 , GLU C:145 , HIS C:146
BINDING SITE FOR RESIDUE SO4 C 513
14
BC5
SOFTWARE
SER D:204 , GLN D:206 , ARG D:227 , ARG D:235 , HIS D:236 , LEU D:237 , TYR D:240 , HIS D:242 , GLU D:244 , TYR D:351 , GLU D:374 , ILE D:375 , ARG D:381 , TYR D:419 , GLY D:420 , LEU D:421 , GLY D:422 , ARG D:425
BINDING SITE FOR RESIDUE 4AD D 500
15
BC6
SOFTWARE
HIS B:358 , PRO D:132 , MET D:135 , ARG D:232 , TYR D:445 , ARG D:448
BINDING SITE FOR RESIDUE SO4 D 511
16
BC7
SOFTWARE
LYS D:134 , ARG D:437 , LYS D:438
BINDING SITE FOR RESIDUE SO4 D 512
17
BC8
SOFTWARE
TYR D:35 , SER D:144 , GLU D:145 , HIS D:146
BINDING SITE FOR RESIDUE SO4 D 513
18
BC9
SOFTWARE
GLN C:174 , ARG D:154 , GLU D:239 , GLU D:424 , TYR D:442
BINDING SITE FOR RESIDUE GOL D 521
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_tRNA_anti_3m4pD01 (D:28-114)
1b: PFAM_tRNA_anti_3m4pD02 (D:28-114)
1c: PFAM_tRNA_anti_3m4pD03 (D:28-114)
1d: PFAM_tRNA_anti_3m4pD04 (D:28-114)
2a: PFAM_tRNA_synt_2_3m4pD05 (D:130-446)
2b: PFAM_tRNA_synt_2_3m4pD06 (D:130-446)
2c: PFAM_tRNA_synt_2_3m4pD07 (D:130-446)
2d: PFAM_tRNA_synt_2_3m4pD08 (D:130-446)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
OB
(224)
Family
:
tRNA_anti
(18)
Entamoeba histolytica
(2)
1a
tRNA_anti-3m4pD01
D:28-114
1b
tRNA_anti-3m4pD02
D:28-114
1c
tRNA_anti-3m4pD03
D:28-114
1d
tRNA_anti-3m4pD04
D:28-114
Clan
:
tRNA_synt_II
(64)
Family
:
tRNA-synt_2
(8)
Entamoeba histolytica
(2)
2a
tRNA-synt_2-3m4pD05
D:130-446
2b
tRNA-synt_2-3m4pD06
D:130-446
2c
tRNA-synt_2-3m4pD07
D:130-446
2d
tRNA-synt_2-3m4pD08
D:130-446
[
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
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 (607 KB)
Header - Asym.Unit
Biol.Unit 1 (304 KB)
Header - Biol.Unit 1
Biol.Unit 2 (301 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
3M4P
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help