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.
1GUA
Asym. Unit
Info
Asym.Unit (47 KB)
Biol.Unit 1 (43 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN RAP1A, RESIDUES 1-167, DOUBLE MUTANT (E30D,K31E) COMPLEXED WITH GPPNHP AND THE RAS-BINDING-DOMAIN OF HUMAN C-RAF1, RESIDUES 51-131
Authors
:
N. Nassar, A. Wittinghofer
Date
:
18 Jun 96 (Deposition) - 11 Jan 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oncogene Protein/Kinase/Effector Protein Gtp-Binding- Protein, Complex (Gtp-Binding/Atp-Binding)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Nassar, G. Horn, C. Herrmann, C. Block, R. Janknecht, A. Wittinghofer
Ras/Rap Effector Specificity Determined By Charge Reversal.
Nat. Struct. Biol. V. 3 723 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
GNP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:17 , THR A:35 , GNP A:170 , HOH A:501 , HOH A:502
BINDING SITE FOR RESIDUE MG A 171
2
AC2
SOFTWARE
ASP B:80 , GLY B:123 , GLU B:125 , HOH B:517 , HOH B:531 , HOH B:574
BINDING SITE FOR RESIDUE CA B 132
3
AC3
SOFTWARE
GLY A:12 , GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , ASP A:30 , GLU A:31 , PRO A:34 , THR A:35 , GLN A:50 , GLY A:60 , ASN A:116 , LYS A:117 , ASP A:119 , SER A:147 , ALA A:148 , MG A:171 , HOH A:501 , HOH A:503 , HOH A:526 , HOH A:537
BINDING SITE FOR RESIDUE GNP A 170
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: RAS (A:1-167)
2: RBD (B:56-131)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAS
PS51421
small GTPase Ras family profile.
RAP1A_HUMAN
1-184
1
A:1-167
2
RBD
PS50898
Ras-binding domain (RBD) profile.
RAF1_HUMAN
56-131
1
B:56-131
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.2 (B:56-69)
Exon 1.3a (B:70-107)
Exon 1.4 (B:107-131)
Exon 2.4b (A:1-19)
Exon 2.5 (A:20-42)
Exon 2.6 (A:43-61)
Exon 2.7 (A:62-108)
Exon 2.8b (A:109-156)
Exon 2.10 (A:157-167)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3a
03: Boundary 1.3a/1.4
04: Boundary 1.4/1.5a
05: Boundary 2.2b/2.4b
06: Boundary 2.4b/2.5
07: Boundary 2.5/2.6
08: Boundary 2.6/2.7
09: Boundary 2.7/2.8b
10: Boundary 2.8b/2.10
11: Boundary 2.10/2.11d
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
1.1a
ENST00000251849
1a
ENSE00001162426
chr3:
12705725-12705312
414
RAF1_HUMAN
-
0
0
-
-
1.2
ENST00000251849
2
ENSE00000966590
chr3:
12660246-12660014
233
RAF1_HUMAN
1-69
69
1
B:56-69
14
1.3a
ENST00000251849
3a
ENSE00000966591
chr3:
12653561-12653449
113
RAF1_HUMAN
70-107
38
1
B:70-107
38
1.4
ENST00000251849
4
ENSE00001712492
chr3:
12650834-12650732
103
RAF1_HUMAN
107-141
35
1
B:107-131
25
1.5a
ENST00000251849
5a
ENSE00001694126
chr3:
12650422-12650265
158
RAF1_HUMAN
142-194
53
0
-
-
1.6
ENST00000251849
6
ENSE00001594348
chr3:
12647798-12647700
99
RAF1_HUMAN
194-227
34
0
-
-
1.7a
ENST00000251849
7a
ENSE00001732694
chr3:
12645788-12645635
154
RAF1_HUMAN
227-278
52
0
-
-
1.9a
ENST00000251849
9a
ENSE00001725784
chr3:
12641914-12641887
28
RAF1_HUMAN
279-288
10
0
-
-
1.9c
ENST00000251849
9c
ENSE00001703663
chr3:
12641778-12641651
128
RAF1_HUMAN
288-330
43
0
-
-
1.10a
ENST00000251849
10a
ENSE00001609464
chr3:
12641307-12641190
118
RAF1_HUMAN
331-370
40
0
-
-
1.12c
ENST00000251849
12c
ENSE00001683112
chr3:
12633291-12633207
85
RAF1_HUMAN
370-398
29
0
-
-
1.13a
ENST00000251849
13a
ENSE00001651042
chr3:
12632473-12632297
177
RAF1_HUMAN
398-457
60
0
-
-
1.14a
ENST00000251849
14a
ENSE00001803276
chr3:
12629136-12629090
47
RAF1_HUMAN
457-473
17
0
-
-
1.15b
ENST00000251849
15b
ENSE00001610290
chr3:
12627298-12627180
119
RAF1_HUMAN
473-512
40
0
-
-
1.16
ENST00000251849
16
ENSE00001758370
chr3:
12626752-12626621
132
RAF1_HUMAN
513-556
44
0
-
-
1.17
ENST00000251849
17
ENSE00001748764
chr3:
12626480-12626346
135
RAF1_HUMAN
557-601
45
0
-
-
1.18e
ENST00000251849
18e
ENSE00001671036
chr3:
12626156-12625100
1057
RAF1_HUMAN
602-648
47
0
-
-
2.2b
ENST00000369709
2b
ENSE00001301159
chr1:
112162405-112162556
152
RAP1A_HUMAN
-
0
0
-
-
2.4b
ENST00000369709
4b
ENSE00002192286
chr1:
112233956-112234039
84
RAP1A_HUMAN
1-19
19
1
A:1-19
19
2.5
ENST00000369709
5
ENSE00001743787
chr1:
112237963-112238031
69
RAP1A_HUMAN
20-42
23
1
A:20-42
23
2.6
ENST00000369709
6
ENSE00000783725
chr1:
112240063-112240119
57
RAP1A_HUMAN
43-61
19
1
A:43-61
19
2.7
ENST00000369709
7
ENSE00001775049
chr1:
112245958-112246098
141
RAP1A_HUMAN
62-108
47
1
A:62-108
47
2.8b
ENST00000369709
8b
ENSE00001675702
chr1:
112246965-112247108
144
RAP1A_HUMAN
109-156
48
1
A:109-156
48
2.10
ENST00000369709
10
ENSE00000826954
chr1:
112251771-112251886
116
RAP1A_HUMAN
157-184
28
1
A:157-167
11
2.11d
ENST00000369709
11d
ENSE00001835102
chr1:
112255053-112259313
4261
RAP1A_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1guab_ (B:)
2a: SCOP_d1guaa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ras-binding domain, RBD
(83)
Protein domain
:
c-Raf1 RBD
(7)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1guab_
B:
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
:
Rap1A
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d1guaa_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1guaA00 (A:1-167)
2a: CATH_1guaB00 (B:56-131)
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)
Human (Homo sapiens)
(413)
1a
1guaA00
A:1-167
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
(286)
Human (Homo sapiens)
(177)
2a
1guaB00
B:56-131
[
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 (47 KB)
Header - Asym.Unit
Biol.Unit 1 (43 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
1GUA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help