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.
4KAX
Asym. Unit
Info
Asym.Unit (69 KB)
Biol.Unit 1 (63 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 THE GRP1 PH DOMAIN IN COMPLEX WITH ARF6-GTP
Authors
:
D. G. Lambright, A. W. Malaby, B. Van Den Berg
Date
:
23 Apr 13 (Deposition) - 14 Aug 13 (Release) - 11 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Ph Domain, Phosphoinositides, Protein Binding-Signaling Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. W. Malaby, B. Van Den Berg, D. G. Lambright
Structural Basis For Membrane Recruitment And Allosteric Activation Of Cytohesin Family Arf Gtpase Exchange Factors.
Proc. Natl. Acad. Sci. Usa V. 110 14213 2013
[
close entry info
]
Hetero Components
(6, 9)
Info
All Hetero Components
1a: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHA... (4IPa)
2a: CITRIC ACID (CITa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
4a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
5a: POTASSIUM ION (Ka)
6a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4IP
1
Ligand/Ion
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2
CIT
1
Ligand/Ion
CITRIC ACID
3
GOL
4
Ligand/Ion
GLYCEROL
4
GTP
1
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
5
K
1
Ligand/Ion
POTASSIUM ION
6
MG
1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:22 , ALA A:23 , ALA A:24 , GLY A:25 , LYS A:26 , THR A:27 , THR A:28 , THR A:41 , THR A:44 , GLY A:66 , ASN A:122 , LYS A:123 , ASP A:125 , LEU A:126 , CYS A:155 , ALA A:156 , MG A:202 , HOH A:311 , HOH A:314 , HOH A:323 , HOH A:329 , HOH A:340 , HOH A:342 , HOH A:353 , HOH A:354 , HOH A:355 , HOH A:388 , HOH A:414
BINDING SITE FOR RESIDUE GTP A 201
2
AC2
SOFTWARE
THR A:27 , THR A:44 , GTP A:201 , HOH A:354 , HOH A:355
BINDING SITE FOR RESIDUE MG A 202
3
AC3
SOFTWARE
LYS A:34 , THR A:51 , THR A:53 , LYS A:55 , LYS A:58 , GOL A:204 , HOH A:349 , HOH A:371 , HOH A:389 , HOH A:420 , ALA B:396 , ASN B:397
BINDING SITE FOR RESIDUE CIT A 203
4
AC4
SOFTWARE
LEU A:33 , LYS A:34 , VAL A:52 , THR A:53 , LYS A:55 , TYR A:163 , CIT A:203 , HOH A:341 , HOH A:344
BINDING SITE FOR RESIDUE GOL A 204
5
AC5
SOFTWARE
HIS A:76 , THR A:79 , HOH A:359 , HOH A:364 , GLY B:348 , HOH B:1281
BINDING SITE FOR RESIDUE K A 205
6
AC6
SOFTWARE
LYS B:273 , GLY B:275 , GLY B:276 , ARG B:277 , VAL B:278 , THR B:280 , LYS B:282 , ARG B:284 , TYR B:295 , ARG B:305 , LYS B:343 , ASN B:354 , HIS B:355 , HOH B:1201 , HOH B:1211 , HOH B:1215 , HOH B:1221 , HOH B:1226 , HOH B:1247 , HOH B:1252 , HOH B:1263 , HOH B:1293 , HOH B:1301 , HOH B:1305 , HOH B:1356
BINDING SITE FOR RESIDUE 4IP B 1101
7
AC7
SOFTWARE
ASP A:94 , TRP B:281 , ASP B:320 , ARG B:322 , ARG B:359 , HOH B:1265 , HOH B:1272 , HOH B:1275
BINDING SITE FOR RESIDUE GOL B 1102
8
AC8
SOFTWARE
LYS A:69 , PHE B:263 , ASN B:264 , ASP B:266 , THR B:289 , ASP B:290
BINDING SITE FOR RESIDUE GOL B 1103
9
AC9
SOFTWARE
THR B:259 , TRP B:285 , ILE B:287 , THR B:299 , ASP B:301 , HOH B:1358 , HOH B:1374 , HOH B:1387
BINDING SITE FOR RESIDUE GOL B 1104
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d4kaxb_ (B:)
2a: SCOP_d4kaxa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PH domain-like barrel
(258)
Superfamily
:
PH domain-like
(257)
Family
:
Pleckstrin-homology domain (PH domain)
(102)
Protein domain
:
automated matches
(10)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d4kaxb_
B:
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
:
ADP-ribosylation factor
(40)
Human (Homo sapiens), ARF1 [TaxId: 9606]
(12)
2a
d4kaxa_
A:
[
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
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 (69 KB)
Header - Asym.Unit
Biol.Unit 1 (63 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
4KAX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
