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Asym. Unit
Info
Asym.Unit (46 KB)
Biol.Unit 1 (108 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GPPNHP
Authors
:
B. U. Klink, R. S. Goody, A. J. Scheidig
Date
:
25 Apr 06 (Deposition) - 31 May 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : X
Biol. Unit 1: X (3x)
Keywords
:
Nucleotide Binding Protein, Methylation, Lipoprotein, Gtp-Binding, Fluorescence, Gppnhp, Membrane, Palmitate, Prenylation, Proto-Oncogene, Golgi Apparatus, Disease Mutation, Nucleotide-Binding, Guanine Nucleotide Binding Protein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. U. Klink, R. S. Goody, A. J. Scheidig
A Newly Designed Microspectrofluorometer For Kinetic Studies On Protein Crystals In Combination With X-Ray Diffraction
Biophys. J. V. 91 981 2006
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
3a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
4a: N,N'-DIMETHYL-N-(ACETYL)-N'-(7-NIT... (XY2a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GNP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2
MG
5
Ligand/Ion
MAGNESIUM ION
3
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4
XY2
1
Ligand/Ion
N,N'-DIMETHYL-N-(ACETYL)-N'-(7-NITROBENZ-2-OXA-1,3-DIAZOL-4-YL)ETHYLENEDIAMINE
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH X:2110 , HOH X:2119
BINDING SITE FOR RESIDUE MG X 167
2
AC2
SOFTWARE
SER X:17 , GNP X:200 , HOH X:2034 , HOH X:2067 , HOH X:2161
BINDING SITE FOR RESIDUE MG X 168
3
AC3
SOFTWARE
ASP X:132 , HOH X:2112 , HOH X:2113 , HOH X:2121 , HOH X:2122 , HOH X:2123
BINDING SITE FOR RESIDUE MG X 169
4
AC4
SOFTWARE
GLU X:63 , GNP X:200 , HOH X:2030 , HOH X:2035 , HOH X:2072 , HOH X:2074
BINDING SITE FOR RESIDUE MG X 170
5
AC5
SOFTWARE
GLN X:165 , HOH X:2041 , HOH X:2132 , HOH X:2155 , HOH X:2156
BINDING SITE FOR RESIDUE MG X 171
6
AC6
SOFTWARE
GLN X:25 , ASP X:38 , SER X:39 , TYR X:40 , HOH X:2159 , HOH X:2160
BINDING SITE FOR RESIDUE TRS X 199
7
AC7
SOFTWARE
GLY X:12 , GLY X:13 , VAL X:14 , GLY X:15 , LYS X:16 , SER X:17 , ALA X:18 , PHE X:28 , VAL X:29 , ASP X:30 , GLU X:31 , ASP X:33 , GLY X:60 , GLU X:63 , ASN X:116 , LYS X:117 , ASP X:119 , LEU X:120 , SER X:145 , ALA X:146 , LYS X:147 , MG X:168 , MG X:170 , XY2 X:332 , HOH X:2027 , HOH X:2030 , HOH X:2034 , HOH X:2035 , HOH X:2067 , HOH X:2072 , HOH X:2073 , HOH X:2161 , HOH X:2165 , HOH X:2166
BINDING SITE FOR RESIDUE GNP X 200
8
AC8
SOFTWARE
GLU X:31 , CYS X:32 , GNP X:200 , HOH X:2017
BINDING SITE FOR RESIDUE XY2 X 332
[
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]
SAPs(SNPs)/Variants
(17, 17)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_026106 (G12A, chain X, )
02: VAR_045975 (G12C, chain X, )
03: VAR_068816 (G12D, chain X, )
04: VAR_045976 (G12E, chain X, )
05: VAR_006837 (G12S, chain X, )
06: VAR_006836 (G12V, chain X, )
07: VAR_026107 (G13C, chain X, )
08: VAR_026108 (G13D, chain X, )
09: VAR_068817 (G13R, chain X, )
10: VAR_045977 (Q22K, chain X, )
11: VAR_045978 (T58I, chain X, )
12: VAR_045979 (Q61K, chain X, )
13: VAR_006838 (Q61L, chain X, )
14: VAR_045980 (E63K, chain X, )
15: VAR_045981 (K117R, chain X, )
16: VAR_045982 (A146T, chain X, )
17: VAR_045983 (A146V, chain X, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_026106
G
12
A
RASH_HUMAN
Disease (CSTLO)
---
X
G
12
A
02
UniProt
VAR_045975
G
12
C
RASH_HUMAN
Disease (CSTLO)
---
X
G
12
C
03
UniProt
VAR_068816
G
12
D
RASH_HUMAN
Disease (CSTLO)
---
X
G
12
D
04
UniProt
VAR_045976
G
12
E
RASH_HUMAN
Disease (CSTLO)
---
X
G
12
E
05
UniProt
VAR_006837
G
12
S
RASH_HUMAN
Disease (CSTLO)
---
X
G
12
S
06
UniProt
VAR_006836
G
12
V
RASH_HUMAN
Disease (CSTLO)
---
X
G
12
V
07
UniProt
VAR_026107
G
13
C
RASH_HUMAN
Disease (CSTLO)
---
X
G
13
C
08
UniProt
VAR_026108
G
13
D
RASH_HUMAN
Disease (CSTLO)
---
X
G
13
D
09
UniProt
VAR_068817
G
13
R
RASH_HUMAN
Disease (SFM)
---
X
G
13
R
10
UniProt
VAR_045977
Q
22
K
RASH_HUMAN
Disease (CMEMS)
---
X
Q
22
K
11
UniProt
VAR_045978
T
58
I
RASH_HUMAN
Disease (CSTLO)
---
X
T
58
I
12
UniProt
VAR_045979
Q
61
K
RASH_HUMAN
Unclassified
28933406
X
Q
61
K
13
UniProt
VAR_006838
Q
61
L
RASH_HUMAN
Unclassified
---
X
Q
61
L
14
UniProt
VAR_045980
E
63
K
RASH_HUMAN
Disease (CMEMS)
---
X
E
63
K
15
UniProt
VAR_045981
K
117
R
RASH_HUMAN
Disease (CSTLO)
---
X
K
117
R
16
UniProt
VAR_045982
A
146
T
RASH_HUMAN
Disease (CSTLO)
---
X
A
146
T
17
UniProt
VAR_045983
A
146
V
RASH_HUMAN
Disease (CSTLO)
---
X
A
146
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RAS (X:1-166)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAS
PS51421
small GTPase Ras family profile.
RASH_HUMAN
1-188
1
X:1-166
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.5b (X:1-37)
Exon 1.6c (X:38-97)
Exon 1.7a (X:97-150)
Exon 1.9d (X:151-166)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.5b
2: Boundary 1.5b/1.6c
3: Boundary 1.6c/1.7a
4: Boundary 1.7a/1.9d
5: Boundary 1.9d/-
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
1.3
ENST00000397596
3
ENSE00001529352
chr11:
535339-535257
83
RASH_HUMAN
-
0
0
-
-
1.5b
ENST00000397596
5b
ENSE00002189675
chr11:
534375-534212
164
RASH_HUMAN
1-37
37
1
X:1-37
37
1.6c
ENST00000397596
6c
ENSE00001728710
chr11:
533944-533766
179
RASH_HUMAN
38-97
60
1
X:38-97
60
1.7a
ENST00000397596
7a
ENSE00001206466
chr11:
533612-533453
160
RASH_HUMAN
97-150
54
1
X:97-150
54
1.9d
ENST00000397596
9d
ENSE00001628271
chr11:
532755-532242
514
RASH_HUMAN
151-189
39
1
X:151-166
16
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2cl0x_ (X:)
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
:
automated matches
(173)
Human (Homo sapiens) [TaxId: 9606]
(112)
1a
d2cl0x_
X:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2cl0X00 (X:1-166)
View:
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Classes
(
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)
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
2cl0X00
X:1-166
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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Atom Selection
(currently selected atoms:
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Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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