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.
1VG1
Asym. Unit
Info
Asym.Unit (36 KB)
Biol.Unit 1 (32 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
GDP-BOUND RAB7
Authors
:
A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov
Date
:
22 Apr 04 (Deposition) - 20 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Gtp-Binding Protein, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov
Structure Of The Rab7:Rep-1 Complex: Insights Into The Mechanism Of Rab Prenylation And Choroideremia Disease
Cell(Cambridge, Mass. ) V. 117 749 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:22 , HOH A:1085 , HOH A:1087 , HOH A:1088 , HOH A:1153 , GDP A:1557
BINDING SITE FOR RESIDUE MG A 3000
2
AC2
SOFTWARE
GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , THR A:22 , SER A:23 , PHE A:33 , ASN A:125 , LYS A:126 , ASP A:128 , LEU A:129 , SER A:155 , ALA A:156 , LYS A:157 , HOH A:1033 , HOH A:1048 , HOH A:1085 , HOH A:1087 , HOH A:1088 , HOH A:1091 , MG A:3000
BINDING SITE FOR RESIDUE GDP A 1557
[
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
(5, 5)
Info
All Exons
Exon 1.1 (A:5-18)
Exon 1.2 (A:18-60 (gaps))
Exon 1.3 (A:61-133 (gaps))
Exon 1.4 (A:134-176)
Exon 1.5 (A:177-185)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSRNOT00000016432
1
ENSRNOE00000116420
chr4:
122220655-122220588
68
RAB7A_RAT
1-18
18
1
A:5-18
14
1.2
ENSRNOT00000016432
2
ENSRNOE00000116592
chr4:
122217534-122217408
127
RAB7A_RAT
18-60
43
1
A:18-60 (gaps)
43
1.3
ENSRNOT00000016432
3
ENSRNOE00000116782
chr4:
122208992-122208774
219
RAB7A_RAT
61-133
73
1
A:61-133 (gaps)
73
1.4
ENSRNOT00000016432
4
ENSRNOE00000116963
chr4:
122208105-122207977
129
RAB7A_RAT
134-176
43
1
A:134-176
43
1.5
ENSRNOT00000016432
5
ENSRNOE00000117137
chr4:
122204075-122202697
1379
RAB7A_RAT
177-207
31
1
A:177-185
9
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1vg1a_ (A:)
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
:
Rab7
(6)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(4)
1a
d1vg1a_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1vg1A00 (A:5-185)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Norway rat (Rattus norvegicus)
(38)
1a
1vg1A00
A:5-185
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Ras_1vg1A01 (A:10-175)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Rattus norvegicus (Rat)
(6)
1a
Ras-1vg1A01
A:10-175
[
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 (36 KB)
Header - Asym.Unit
Biol.Unit 1 (32 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
1VG1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
