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.
1S8F
Asym. Unit
Info
Asym.Unit (68 KB)
Biol.Unit 1 (33 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (123 KB)
Biol.Unit 4 (63 KB)
Biol.Unit 5 (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 RAB9 COMPLEXED TO GDP REVEALS A DIMER WITH AN ACTIVE CONFORMATION OF SWITCH II
Authors
:
J. G. Wittmann, M. G. Rudolph
Date
:
02 Feb 04 (Deposition) - 11 Jun 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (2x)
Biol. Unit 4: A,B (1x)
Biol. Unit 5: B (2x)
Keywords
:
Intracellular Transport, Vesicular Trafficking, Hemihedral Twinning, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. G. Wittmann, M. G. Rudolph
Crystal Structure Of Rab9 Complexed To Gdp Reveals A Dimer With An Active Conformation Of Switch Ii.
Febs Lett. V. 568 23 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 10)
Info
All Hetero Components
1a: BENZOIC ACID (BEZa)
1b: BENZOIC ACID (BEZb)
1c: BENZOIC ACID (BEZc)
1d: BENZOIC ACID (BEZd)
2a: CHLORIDE ION (CLa)
3a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
3b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
4a: MAGNESIUM ION (MGa)
5a: STRONTIUM ION (SRa)
5b: STRONTIUM ION (SRb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BEZ
4
Ligand/Ion
BENZOIC ACID
2
CL
1
Ligand/Ion
CHLORIDE ION
3
GDP
2
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
SR
2
Ligand/Ion
STRONTIUM 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
SER A:1021 , BEZ A:1502 , GDP A:3400 , HOH A:9005 , HOH A:9009 , HOH A:9024
BINDING SITE FOR RESIDUE SR A 2401
02
AC2
SOFTWARE
SER B:4021 , GDP B:6400 , HOH B:9007 , HOH B:9015 , HOH B:9019 , HOH B:9033
BINDING SITE FOR RESIDUE MG B 5401
03
AC3
SOFTWARE
PHE B:4069 , ARG B:4070 , SER B:4071
BINDING SITE FOR RESIDUE SR B 2001
04
AC4
SOFTWARE
ARG B:4070 , ARG B:4073 , THR B:4074 , HOH B:9011 , HOH B:9069
BINDING SITE FOR RESIDUE CL B 3001
05
AC5
SOFTWARE
GLY A:1017 , VAL A:1018 , GLY A:1019 , LYS A:1020 , SER A:1021 , SER A:1022 , PHE A:1032 , ASN A:1124 , LYS A:1125 , ASP A:1127 , ILE A:1128 , SER A:1154 , ALA A:1155 , LYS A:1156 , BEZ A:1502 , SR A:2401 , HOH A:9009 , HOH A:9024 , HOH A:9026 , HOH A:9081 , HOH A:9085 , HOH A:9152 , HOH A:9224
BINDING SITE FOR RESIDUE GDP A 3400
06
AC6
SOFTWARE
GLY B:4017 , VAL B:4018 , GLY B:4019 , LYS B:4020 , SER B:4021 , SER B:4022 , PHE B:4032 , ASN B:4124 , LYS B:4125 , ASP B:4127 , SER B:4154 , ALA B:4155 , LYS B:4156 , MG B:5401 , HOH B:9007 , HOH B:9019 , HOH B:9033 , HOH B:9095 , HOH B:9145 , HOH B:9150 , HOH B:9219
BINDING SITE FOR RESIDUE GDP B 6400
07
AC7
SOFTWARE
ARG A:1068 , PHE A:1069 , ARG A:1070 , SER A:1071 , LEU A:1072 , BEZ A:1501 , HOH A:9103 , SER B:4071 , HOH B:9043
BINDING SITE FOR RESIDUE BEZ A 1500
08
AC8
SOFTWARE
PHE A:1055 , ARG A:1068 , BEZ A:1500 , HOH A:9023 , HOH A:9048 , HOH A:9116 , PRO B:4075 , HOH B:9017
BINDING SITE FOR RESIDUE BEZ A 1501
09
AC9
SOFTWARE
HIS A:1038 , THR A:1039 , GLN A:1066 , SR A:2401 , GDP A:3400 , HOH A:9009 , HOH A:9010 , HOH A:9024 , HOH A:9054
BINDING SITE FOR RESIDUE BEZ A 1502
10
BC1
SOFTWARE
THR B:4063 , GLU B:4067 , ARG B:4068 , PHE B:4069 , ARG B:4070 , ARG B:4073 , HOH B:9110
BINDING SITE FOR RESIDUE BEZ B 1503
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RAB (B:4003-4173)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAB
PS51419
small GTPase Rab1 family profile.
RAB9A_CANLF
3-201
1
B:4003-4173
[
close PROSITE info
]
Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:1005-1174 (gaps) | B:4001-4173 (...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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
ENSCAFT00000018660
1
ENSCAFE00000128459
X:10080937-10081545
609
RAB9A_CANLF
1-202
202
2
A:1005-1174 (gaps)
B:4001-4173 (gaps)
170
173
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1s8fa_ (A:)
1b: SCOP_d1s8fb_ (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
:
Rab9a
(3)
Dog (Canis familiaris) [TaxId: 9615]
(1)
1a
d1s8fa_
A:
1b
d1s8fb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1s8fB00 (B:3999-4173)
1b: CATH_1s8fA00 (A:1005-1174)
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)
Dog (Canis lupus familiaris)
(19)
1a
1s8fB00
B:3999-4173
1b
1s8fA00
A:1005-1174
[
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 (68 KB)
Header - Asym.Unit
Biol.Unit 1 (33 KB)
Header - Biol.Unit 1
Biol.Unit 2 (33 KB)
Header - Biol.Unit 2
Biol.Unit 3 (123 KB)
Header - Biol.Unit 3
Biol.Unit 4 (63 KB)
Header - Biol.Unit 4
Biol.Unit 5 (62 KB)
Header - Biol.Unit 5
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
1S8F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
