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.
1DCE
Biol. Unit 2
Info
Asym.Unit (307 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (152 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 RAB GERANYLGERANYLTRANSFERASE FROM RAT BRAIN
Authors
:
H. Zhang, M. C. Seabra, H. Deisenhofer
Date
:
04 Nov 99 (Deposition) - 24 Mar 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Crystal Structure, Rab Geranylgeranyltransferase, 2. 0 A Resolution, N-Formylmethionine, Alpha Subunit, Beta Subunit
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Zhang, M. C. Seabra, J. Deisenhofer
Crystal Structure Of Rab Geranylgeranyltransferase At 2. 0 A Resolution.
Structure Fold. Des. V. 8 241 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: N-FORMYLMETHIONINE (FMEa)
1b: N-FORMYLMETHIONINE (FMEb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
2
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
HIS C:2 , ASP D:238 , CYS D:240 , HIS D:290
BINDING SITE FOR RESIDUE ZN D 950
[
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, 6)
Info
All PROSITE Patterns/Profiles
1: PFTA (C:363-397)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PFTA
PS51147
Protein prenyltransferases alpha subunit repeat profile.
PGTA_RAT
44-78
88-122
124-158
159-193
207-241
363-397
6
-
C:44-78
-
C:88-122
-
C:124-158
-
C:159-193
-
C:207-241
-
C:363-397
[
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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1dcea1 (A:1-241,A:351-443)
1b: SCOP_d1dcec1 (C:1-241,C:351-443)
2a: SCOP_d1dceb_ (B:)
2b: SCOP_d1dced_ (D:)
3a: SCOP_d1dcea2 (A:242-350)
3b: SCOP_d1dcec2 (C:242-350)
4a: SCOP_d1dcea3 (A:444-567)
4b: SCOP_d1dcec3 (C:444-567)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
Protein prenylyltransferase
(68)
Family
:
Protein prenylyltransferase
(68)
Protein domain
:
Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
(2)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
1a
d1dcea1
A:1-241,A:351-443
1b
d1dcec1
C:1-241,C:351-443
Fold
:
alpha/alpha toroid
(324)
Superfamily
:
Terpenoid cyclases/Protein prenyltransferases
(151)
Family
:
Protein prenyltransferases
(86)
Protein domain
:
Rab geranylgeranyltransferase, beta subunit
(21)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(21)
2a
d1dceb_
B:
2b
d1dced_
D:
Class
:
All beta proteins
(24004)
Fold
:
C2 domain-like
(198)
Superfamily
:
Rab geranylgeranyltransferase alpha-subunit, insert domain
(2)
Family
:
Rab geranylgeranyltransferase alpha-subunit, insert domain
(2)
Protein domain
:
Rab geranylgeranyltransferase alpha-subunit, insert domain
(2)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
3a
d1dcea2
A:242-350
3b
d1dcec2
C:242-350
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(112)
Superfamily
:
L domain-like
(93)
Family
:
Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
(2)
Protein domain
:
Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
(2)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
4a
d1dcea3
A:444-567
4b
d1dcec3
C:444-567
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1dceA03 (A:431-566)
1b: CATH_1dceC03 (C:431-566)
2a: CATH_1dceA01 (A:2-241,A:353-429)
2b: CATH_1dceC01 (C:2-241,C:353-429)
3a: CATH_1dceB00 (B:3-331)
3b: CATH_1dceD00 (D:3-331)
4a: CATH_1dceA02 (A:242-344)
4b: CATH_1dceC02 (C:242-344)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Horseshoe
(92)
Topology
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(73)
Homologous Superfamily
:
Ribonuclease Inhibitor
(73)
Norway rat (Rattus norvegicus)
(2)
1a
1dceA03
A:431-566
1b
1dceC03
C:431-566
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha Horseshoe
(399)
Topology
:
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
(320)
Homologous Superfamily
:
[code=1.25.40.120, no name defined]
(62)
Norway rat (Rattus norvegicus)
(37)
2a
1dceA01
A:2-241,A:353-429
2b
1dceC01
C:2-241,C:353-429
Architecture
:
Alpha/alpha barrel
(251)
Topology
:
Glycosyltransferase
(233)
Homologous Superfamily
:
[code=1.50.10.20, no name defined]
(105)
Norway rat (Rattus norvegicus)
(39)
3a
1dceB00
B:3-331
3b
1dceD00
D:3-331
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.1130, no name defined]
(2)
Norway rat (Rattus norvegicus)
(2)
4a
1dceA02
A:242-344
4b
1dceC02
C:242-344
[
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 C
Chain D
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 (307 KB)
Header - Asym.Unit
Biol.Unit 1 (153 KB)
Header - Biol.Unit 1
Biol.Unit 2 (152 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
1DCE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
