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1R4A
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (148 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GTP-BOUND ADP-RIBOSYLATION FACTOR LIKE PROTEIN 1 (ARL1) AND GRIP DOMAIN OF GOLGIN245 COMPLEX
Authors
:
M. Wu, L. Lu, W. Hong, H. Song
Date
:
04 Oct 03 (Deposition) - 13 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Ras-Like G Protein Structure, Three-Helix Grip Domain, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Wu, L. Lu, W. Hong, H. Song
Structural Basis For Recruitment Of Grip Domain Golgin-245 By Small Gtpase Arl1.
Nat. Struct. Mol. Biol. V. 11 86 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPc)
1d: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GNP
4
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2
MG
4
Ligand/Ion
MAGNESIUM ION
[
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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
THR A:31 , THR A:45 , ILE A:46 , THR A:48 , GNP A:1201
BINDING SITE FOR RESIDUE MG A 901
2
AC2
SOFTWARE
THR B:31 , ILE B:46 , THR B:48 , GNP B:1202 , HOH B:1203
BINDING SITE FOR RESIDUE MG B 902
3
AC3
SOFTWARE
THR C:31 , ILE C:46 , THR C:48 , GNP C:1203 , HOH C:1260
BINDING SITE FOR RESIDUE MG C 903
4
AC4
SOFTWARE
THR D:31 , ILE D:46 , THR D:48 , GNP D:1204
BINDING SITE FOR RESIDUE MG D 904
5
AC5
SOFTWARE
GLY A:27 , ALA A:28 , GLY A:29 , LYS A:30 , THR A:31 , THR A:32 , VAL A:43 , THR A:45 , THR A:48 , GLY A:69 , GLY A:70 , ASN A:126 , LYS A:127 , ASP A:129 , MET A:130 , SER A:159 , ALA A:160 , THR A:161 , MG A:901 , HOH A:1203
BINDING SITE FOR RESIDUE GNP A 1201
6
AC6
SOFTWARE
GLY B:27 , ALA B:28 , GLY B:29 , LYS B:30 , THR B:31 , THR B:32 , VAL B:43 , THR B:45 , THR B:48 , GLY B:69 , GLY B:70 , ASN B:126 , LYS B:127 , ASP B:129 , SER B:159 , ALA B:160 , THR B:161 , MG B:902 , HOH B:1203
BINDING SITE FOR RESIDUE GNP B 1202
7
AC7
SOFTWARE
ASP C:26 , GLY C:27 , ALA C:28 , GLY C:29 , LYS C:30 , THR C:31 , THR C:32 , VAL C:43 , THR C:45 , THR C:48 , GLY C:69 , GLY C:70 , ASN C:126 , LYS C:127 , ASP C:129 , SER C:159 , ALA C:160 , THR C:161 , MG C:903 , HOH C:1218 , HOH C:1223 , HOH C:1260
BINDING SITE FOR RESIDUE GNP C 1203
8
AC8
SOFTWARE
ASP D:26 , GLY D:27 , ALA D:28 , GLY D:29 , LYS D:30 , THR D:31 , THR D:32 , VAL D:43 , THR D:45 , THR D:48 , GLY D:70 , ASN D:126 , LYS D:127 , ASP D:129 , MET D:130 , SER D:159 , ALA D:160 , THR D:161 , MG D:904 , HOH D:1207 , HOH D:1248
BINDING SITE FOR RESIDUE GNP D 1204
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(8, 32)
Info
All Exons
Exon 1.2 (A:16-48 | B:16-48 | C:16-48 | D:16...)
Exon 1.3 (A:48-75 | B:48-75 | C:48-75 | D:48...)
Exon 1.4 (A:75-112 | B:75-112 | C:75-112 | D...)
Exon 1.7a (A:113-175 | B:113-175 | C:113-175 ...)
Exon 1.8 (A:175-180 | B:175-180 | C:175-180 ...)
Exon 2.27 (E:2172-2192 | F:2172-2192 | G:2172...)
Exon 2.28 (E:2193-2221 | F:2193-2221 | G:2193...)
Exon 2.29b (E:2222-2222 | F:2222-2222 | G:2222...)
View:
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Label:
All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.7a
05: Boundary 1.7a/1.8
06: Boundary 1.8/-
07: Boundary 2.26/2.27
08: Boundary 2.27/2.28
09: Boundary 2.28/2.29b
10: Boundary 2.29b/2.30d
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
ENSRNOT00000007623
1
ENSRNOE00000425060
chr7:
25403842-25404017
176
ARL1_RAT
1-2
2
0
-
-
1.2
ENSRNOT00000007623
2
ENSRNOE00000053794
chr7:
25405900-25406037
138
ARL1_RAT
2-48
47
4
A:16-48
B:16-48
C:16-48
D:16-48
33
33
33
33
1.3
ENSRNOT00000007623
3
ENSRNOE00000053965
chr7:
25408414-25408495
82
ARL1_RAT
48-75
28
4
A:48-75
B:48-75
C:48-75
D:48-75
28
28
28
28
1.4
ENSRNOT00000007623
4
ENSRNOE00000054153
chr7:
25409894-25410005
112
ARL1_RAT
75-112
38
4
A:75-112
B:75-112
C:75-112
D:75-112
38
38
38
38
1.7a
ENSRNOT00000007623
7a
ENSRNOE00000242145
chr7:
25415331-25415518
188
ARL1_RAT
113-175
63
4
A:113-175
B:113-175
C:113-175
D:113-175
63
63
63
63
1.8
ENSRNOT00000007623
8
ENSRNOE00000339243
chr7:
25415884-25416893
1010
ARL1_RAT
175-184
10
4
A:175-180
B:175-180
C:175-180
D:175-180
6
6
6
6
2.1a
ENST00000361924
1a
ENSE00001954251
chr3:
37284668-37285113
446
GOGA4_HUMAN
1-24
24
0
-
-
2.4b
ENST00000361924
4b
ENSE00001251040
chr3:
37292886-37292975
90
GOGA4_HUMAN
25-54
30
0
-
-
2.7b
ENST00000361924
7b
ENSE00001251031
chr3:
37323449-37323763
315
GOGA4_HUMAN
55-159
105
0
-
-
2.8
ENST00000361924
8
ENSE00001251023
chr3:
37327505-37327552
48
GOGA4_HUMAN
160-175
16
0
-
-
2.10a
ENST00000361924
10a
ENSE00001251016
chr3:
37330726-37330782
57
GOGA4_HUMAN
176-194
19
0
-
-
2.11a
ENST00000361924
11a
ENSE00001800584
chr3:
37336470-37336568
99
GOGA4_HUMAN
195-227
33
0
-
-
2.12
ENST00000361924
12
ENSE00001663626
chr3:
37337578-37337710
133
GOGA4_HUMAN
228-272
45
0
-
-
2.13
ENST00000361924
13
ENSE00001714886
chr3:
37340324-37340511
188
GOGA4_HUMAN
272-334
63
0
-
-
2.14
ENST00000361924
14
ENSE00001790783
chr3:
37340779-37340862
84
GOGA4_HUMAN
335-362
28
0
-
-
2.15
ENST00000361924
15
ENSE00001758865
chr3:
37343676-37343823
148
GOGA4_HUMAN
363-412
50
0
-
-
2.17b
ENST00000361924
17b
ENSE00001690632
chr3:
37356911-37357089
179
GOGA4_HUMAN
412-471
60
0
-
-
2.18a
ENST00000361924
18a
ENSE00001138663
chr3:
37360554-37360685
132
GOGA4_HUMAN
472-515
44
0
-
-
2.19b
ENST00000361924
19b
ENSE00001138651
chr3:
37363222-37363377
156
GOGA4_HUMAN
516-567
52
0
-
-
2.20c
ENST00000361924
20c
ENSE00001303935
chr3:
37365079-37369316
4238
GOGA4_HUMAN
568-1980
1413
0
-
-
2.21
ENST00000361924
21
ENSE00001250910
chr3:
37369907-37370028
122
GOGA4_HUMAN
1980-2021
42
0
-
-
2.22a
ENST00000361924
22a
ENSE00001250902
chr3:
37370454-37370584
131
GOGA4_HUMAN
2021-2064
44
0
-
-
2.23
ENST00000361924
23
ENSE00001296324
chr3:
37376544-37376657
114
GOGA4_HUMAN
2065-2102
38
0
-
-
2.24
ENST00000361924
24
ENSE00001296753
chr3:
37378634-37378654
21
GOGA4_HUMAN
2103-2109
7
0
-
-
2.25
ENST00000361924
25
ENSE00001315030
chr3:
37379157-37379225
69
GOGA4_HUMAN
2110-2132
23
0
-
-
2.26
ENST00000361924
26
ENSE00001296621
chr3:
37381615-37381690
76
GOGA4_HUMAN
2133-2158
26
0
-
-
2.27
ENST00000361924
27
ENSE00001316090
chr3:
37388684-37388787
104
GOGA4_HUMAN
2158-2192
35
4
E:2172-2192
F:2172-2192
G:2172-2192
H:2172-2192
21
21
21
21
2.28
ENST00000361924
28
ENSE00001298280
chr3:
37396592-37396678
87
GOGA4_HUMAN
2193-2221
29
4
E:2193-2221
F:2193-2221
G:2193-2221
H:2193-2221
29
29
29
29
2.29b
ENST00000361924
29b
ENSE00001435056
chr3:
37402734-37402796
63
GOGA4_HUMAN
2222-2230
9
4
E:2222-2222
F:2222-2222
G:2222-2222
H:2222-2222
1
1
1
1
2.30d
ENST00000361924
30d
ENSE00001673232
chr3:
37407571-37408242
672
GOGA4_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1r4ae_ (E:)
1b: SCOP_d1r4af_ (F:)
1c: SCOP_d1r4ag_ (G:)
1d: SCOP_d1r4ah_ (H:)
2a: SCOP_d1r4aa_ (A:)
2b: SCOP_d1r4ab_ (B:)
2c: SCOP_d1r4ac_ (C:)
2d: SCOP_d1r4ad_ (D:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
GRIP domain
(2)
Superfamily
:
GRIP domain
(2)
Family
:
GRIP domain
(2)
Protein domain
:
Golgi autoantigen, golgin-245
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1r4ae_
E:
1b
d1r4af_
F:
1c
d1r4ag_
G:
1d
d1r4ah_
H:
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
:
ADP-ribosylation factor
(40)
Human (Homo sapiens), ARL1 [TaxId: 9606]
(2)
2a
d1r4aa_
A:
2b
d1r4ab_
B:
2c
d1r4ac_
C:
2d
d1r4ad_
D:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1r4aA00 (A:16-180)
1b: CATH_1r4aB00 (B:16-180)
1c: CATH_1r4aC00 (C:16-180)
1d: CATH_1r4aD00 (D:16-180)
2a: CATH_1r4aE00 (E:2172-2222)
2b: CATH_1r4aF00 (F:2172-2222)
2c: CATH_1r4aG00 (G:2172-2222)
2d: CATH_1r4aH00 (H:2172-2222)
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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)
Norway rat (Rattus norvegicus)
(38)
1a
1r4aA00
A:16-180
1b
1r4aB00
B:16-180
1c
1r4aC00
C:16-180
1d
1r4aD00
D:16-180
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Annexin V; domain 1
(80)
Homologous Superfamily
:
GRIP domain
(2)
Norway rat (Rattus norvegicus)
(1)
2a
1r4aE00
E:2172-2222
2b
1r4aF00
F:2172-2222
2c
1r4aG00
G:2172-2222
2d
1r4aH00
H:2172-2222
[
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]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Arf_1r4aD01 (D:16-177)
1b: PFAM_Arf_1r4aD02 (D:16-177)
1c: PFAM_Arf_1r4aD03 (D:16-177)
1d: PFAM_Arf_1r4aD04 (D:16-177)
2a: PFAM_GRIP_1r4aH01 (H:2172-2213)
2b: PFAM_GRIP_1r4aH02 (H:2172-2213)
2c: PFAM_GRIP_1r4aH03 (H:2172-2213)
2d: PFAM_GRIP_1r4aH04 (H:2172-2213)
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Clan
:
P-loop_NTPase
(1112)
Family
:
Arf
(26)
Rattus norvegicus (Rat)
(3)
1a
Arf-1r4aD01
D:16-177
1b
Arf-1r4aD02
D:16-177
1c
Arf-1r4aD03
D:16-177
1d
Arf-1r4aD04
D:16-177
Clan
:
no clan defined [family: GRIP]
(2)
Family
:
GRIP
(2)
Homo sapiens (Human)
(2)
2a
GRIP-1r4aH01
H:2172-2213
2b
GRIP-1r4aH02
H:2172-2213
2c
GRIP-1r4aH03
H:2172-2213
2d
GRIP-1r4aH04
H:2172-2213
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