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.
4LC0
Asym. Unit
Info
Asym.Unit (143 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (274 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
IDENTIFYING LIGAND BINDING HOT SPOTS IN PROTEINS USING BROMINATED FRAGMENTS
Authors
:
M. K. Groftehauge, M. Therkelsen, R. Taaning, T. Skrydstrup, J. P. Mort P. Nissen
Date
:
21 Jun 13 (Deposition) - 11 Sep 13 (Release) - 11 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.22
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Gtpase, , Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. K. Grftehauge, M. O. Therkelsen, R. Taaning, T. Skrydstrup, J. P. Morth, P. Nissen
Identifying Ligand-Binding Hot Spots In Proteins Using Brominated Fragments.
Acta Crystallogr. , Sect. F V. 69 1060 2013
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
2a: MAGNESIUM ION (MGa)
3a: AMMONIUM ION (NH4a)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GNP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
NH4
1
Ligand/Ion
AMMONIUM ION
4
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:20 , ASP A:21 , HIS A:22 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , TYR A:47 , ILE A:61 , THR A:62 , GLY A:84 , ASN A:136 , LYS A:137 , ASP A:139 , MET A:140 , SER A:174 , ALA A:175 , LEU A:176 , GLN A:354 , MG A:502 , HOH A:606 , HOH A:635 , HOH A:720 , HOH A:721 , HOH A:782 , HOH A:783
BINDING SITE FOR RESIDUE GNP A 501
02
AC2
SOFTWARE
THR A:25 , THR A:62 , GNP A:501 , HOH A:720 , HOH A:721
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
ILE A:50 , ASP A:51 , GLU A:56 , THR A:62 , ASN A:64 , HOH A:602
BINDING SITE FOR RESIDUE NH4 A 503
04
AC4
SOFTWARE
MET A:113 , PRO A:114 , ARG A:117 , HOH A:737 , HOH A:784
BINDING SITE FOR RESIDUE SO4 A 504
05
AC5
SOFTWARE
LYS A:45 , HIS A:67 , HIS A:273 , ARG A:274
BINDING SITE FOR RESIDUE SO4 A 505
06
AC6
SOFTWARE
ARG A:59 , HIS A:85
BINDING SITE FOR RESIDUE SO4 A 506
07
AC7
SOFTWARE
LYS A:248 , ARG A:291 , HOH A:710
BINDING SITE FOR RESIDUE SO4 A 507
08
AC8
SOFTWARE
ARG A:330 , HIS A:331 , THR A:332 , ARG A:393 , HOH A:763
BINDING SITE FOR RESIDUE SO4 A 508
09
AC9
SOFTWARE
ARG A:57 , GLY A:358 , HOH A:634
BINDING SITE FOR RESIDUE SO4 A 509
10
BC1
SOFTWARE
GLN A:181 , ARG A:184
BINDING SITE FOR RESIDUE SO4 A 510
[
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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d4lc0a3 (A:313-405)
2a: SCOP_d4lc0a2 (A:213-312)
3a: SCOP_d4lc0a1 (A:3-212)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Elongation factor/aminomethyltransferase common domain
(82)
Superfamily
:
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
(67)
Family
:
automated matches
(19)
Protein domain
:
automated matches
(19)
Thermus thermophilus [TaxId: 274]
(6)
1a
d4lc0a3
A:313-405
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Translation proteins
(218)
Family
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Thermus thermophilus [TaxId: 274]
(6)
2a
d4lc0a2
A:213-312
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
automated matches
(173)
Thermus thermophilus [TaxId: 274]
(6)
3a
d4lc0a1
A:3-212
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 (143 KB)
Header - Asym.Unit
Biol.Unit 1 (138 KB)
Header - Biol.Unit 1
Biol.Unit 2 (274 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
4LC0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
