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.
3NKV
Biol. Unit 1
Info
Asym.Unit (127 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 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 RAB1B COVALENTLY MODIFIED WITH AMP AT Y77
Authors
:
M. P. Mueller, H. Peters, W. Blankenfeldt, R. S. Goody, A. Itzen
Date
:
21 Jun 10 (Deposition) - 04 Aug 10 (Release) - 22 Sep 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Posttranslational Modification, Ampylation, Adenylylation, Rab1B, Vesicular Transport, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. P. Muller, H. Peters, J. Blumer, W. Blankenfeldt, R. S. Goody, A. Itzen
The Legionella Effector Protein Drra Ampylates The Membrane Traffic Regulator Rab1B.
Science V. 329 946 2010
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
2a: BARIUM ION (BAa)
2b: BARIUM ION (BAb)
3a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
3b: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
BA
-1
Ligand/Ion
BARIUM ION
3
GNP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , SER A:22 , CYS A:23 , TYR A:33 , THR A:34 , GLU A:35 , SER A:36 , SER A:39 , THR A:40 , GLY A:66 , ASN A:121 , LYS A:122 , ASP A:124 , LEU A:125 , SER A:151 , ALA A:152 , LYS A:153 , HOH A:187 , HOH A:189 , HOH A:191 , HOH A:208 , HOH A:211 , HOH A:218 , HOH A:291 , MG A:500
BINDING SITE FOR RESIDUE GNP A 400
2
AC2
SOFTWARE
SER A:22 , THR A:40 , HOH A:189 , HOH A:218 , GNP A:400
BINDING SITE FOR RESIDUE MG A 500
3
AC3
SOFTWARE
ILE A:41 , VAL A:43 , ASP A:44 , HOH A:261
BINDING SITE FOR RESIDUE BA A 175
4
AC4
SOFTWARE
VAL A:43 , PHE A:45 , GLN A:60 , TRP A:62 , TYR A:77 , HOH A:281
BINDING SITE FOR RESIDUE AMP A 600
5
AC7
SOFTWARE
GLU A:4 , ASP A:6 , THR A:56 , ASP B:132 , THR B:134 , HOH B:187 , HOH B:228 , HOH B:301
BINDING SITE FOR RESIDUE BA B 175
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RAB (A:4-173)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAB
PS51419
small GTPase Rab1 family profile.
RAB1B_HUMAN
4-201
1
A:4-173
-
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d3nkva_ (A:)
1b: SCOP_d3nkvb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
Human (Homo sapiens) [TaxId: 9606]
(112)
1a
d3nkva_
A:
1b
d3nkvb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Ras_3nkvB01 (B:10-171)
1b: PFAM_Ras_3nkvB02 (B:10-171)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
1a
Ras-3nkvB01
B:10-171
1b
Ras-3nkvB02
B:10-171
[
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 (127 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 2 (62 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
3NKV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
