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.
1DCE
Asym. Unit
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
(2, 4)
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
2
Mod. Amino Acid
N-FORMYLMETHIONINE
2
ZN
2
Ligand/Ion
ZINC 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
HIS A:2 , ASP B:238 , CYS B:240 , HIS B:290
BINDING SITE FOR RESIDUE ZN B 900
2
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 not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: PFTA (A:44-78,C:44-78|A:88-122,C:88-122|...)
;
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
12
A:44-78
C:44-78
A:88-122
C:88-122
A:124-158
C:124-158
A:159-193
C:159-193
A:207-241
C:207-241
A:363-397
C:363-397
[
close PROSITE info
]
Exons
(16, 32)
Info
All Exons
Exon 1.2 (A:1-1 | C:1-1)
Exon 1.3 (A:2-38 | C:2-38)
Exon 1.4 (A:39-80 | C:39-80)
Exon 1.5 (A:80-143 | C:80-143)
Exon 1.6 (A:143-211 | C:143-211)
Exon 1.7 (A:211-239 | C:211-239)
Exon 1.8 (A:239-266 | C:239-266)
Exon 1.9 (A:267-300 | C:267-300)
Exon 1.10 (A:301-336 | C:301-336)
Exon 1.11 (A:336-353 | C:336-353)
Exon 1.12 (A:353-383 | C:353-383)
Exon 1.13 (A:383-412 | C:383-412)
Exon 1.14 (A:413-451 | C:413-451)
Exon 1.15 (A:452-489 | C:452-489)
Exon 1.16 (A:490-519 | C:490-519)
Exon 1.17 (A:519-567 | C:519-567)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16
16: Boundary 1.16/1.17
17: Boundary 1.17/-
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
ENSRNOT00000048455
1
ENSRNOE00000431461
chr15:
33868619-33868585
35
PGTA_RAT
-
0
0
-
-
1.2
ENSRNOT00000048455
2
ENSRNOE00000442687
chr15:
33868298-33868241
58
PGTA_RAT
1-1
1
2
A:1-1
C:1-1
1
1
1.3
ENSRNOT00000048455
3
ENSRNOE00000336091
chr15:
33868107-33867997
111
PGTA_RAT
2-38
37
2
A:2-38
C:2-38
37
37
1.4
ENSRNOT00000048455
4
ENSRNOE00000290128
chr15:
33867677-33867553
125
PGTA_RAT
39-80
42
2
A:39-80
C:39-80
42
42
1.5
ENSRNOT00000048455
5
ENSRNOE00000303229
chr15:
33867378-33867191
188
PGTA_RAT
80-143
64
2
A:80-143
C:80-143
64
64
1.6
ENSRNOT00000048455
6
ENSRNOE00000290397
chr15:
33866934-33866731
204
PGTA_RAT
143-211
69
2
A:143-211
C:143-211
69
69
1.7
ENSRNOT00000048455
7
ENSRNOE00000327073
chr15:
33866284-33866201
84
PGTA_RAT
211-239
29
2
A:211-239
C:211-239
29
29
1.8
ENSRNOT00000048455
8
ENSRNOE00000288887
chr15:
33866112-33866030
83
PGTA_RAT
239-266
28
2
A:239-266
C:239-266
28
28
1.9
ENSRNOT00000048455
9
ENSRNOE00000339199
chr15:
33865939-33865838
102
PGTA_RAT
267-300
34
2
A:267-300
C:267-300
34
34
1.10
ENSRNOT00000048455
10
ENSRNOE00000352360
chr15:
33865732-33865627
106
PGTA_RAT
301-336
36
2
A:301-336
C:301-336
36
36
1.11
ENSRNOT00000048455
11
ENSRNOE00000303916
chr15:
33865535-33865484
52
PGTA_RAT
336-353
18
2
A:336-353
C:336-353
18
18
1.12
ENSRNOT00000048455
12
ENSRNOE00000357522
chr15:
33865353-33865265
89
PGTA_RAT
353-383
31
2
A:353-383
C:353-383
31
31
1.13
ENSRNOT00000048455
13
ENSRNOE00000294255
chr15:
33865148-33865060
89
PGTA_RAT
383-412
30
2
A:383-412
C:383-412
30
30
1.14
ENSRNOT00000048455
14
ENSRNOE00000306932
chr15:
33864791-33864675
117
PGTA_RAT
413-451
39
2
A:413-451
C:413-451
39
39
1.15
ENSRNOT00000048455
15
ENSRNOE00000363642
chr15:
33864038-33863925
114
PGTA_RAT
452-489
38
2
A:452-489
C:452-489
38
38
1.16
ENSRNOT00000048455
16
ENSRNOE00000281487
chr15:
33863675-33863588
88
PGTA_RAT
490-519
30
2
A:490-519
C:490-519
30
30
1.17
ENSRNOT00000048455
17
ENSRNOE00000307031
chr15:
33862501-33862275
227
PGTA_RAT
519-567
49
2
A:519-567
C:519-567
49
49
[
close EXON info
]
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 A
Chain B
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