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1VG8
Asym. Unit
Info
Asym.Unit (142 KB)
Biol.Unit 1 (37 KB)
Biol.Unit 2 (36 KB)
Biol.Unit 3 (36 KB)
Biol.Unit 4 (37 KB)
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(1)
Title
:
GPPNHP-BOUND RAB7
Authors
:
A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov
Date
:
23 Apr 04 (Deposition) - 20 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Gtp-Binding Protein, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov
Structure Of The Rab7:Rep-1 Complex: Insights Into The Mechanism Of Rab Prenylation And Choroideremia Disease
Cell(Cambridge, Mass. ) V. 117 749 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:1022 , THR A:1040 , GNP A:1400 , HOH A:5002 , HOH A:5314
BINDING SITE FOR RESIDUE MG A 1401
2
AC2
SOFTWARE
THR B:2022 , THR B:2040 , GNP B:2400 , HOH B:5006 , HOH B:5315
BINDING SITE FOR RESIDUE MG B 2401
3
AC3
SOFTWARE
THR C:3022 , THR C:3040 , GNP C:3400 , HOH C:5001 , HOH C:5009
BINDING SITE FOR RESIDUE MG C 3401
4
AC4
SOFTWARE
THR D:4022 , THR D:4040 , GNP D:4400 , HOH D:5003 , HOH D:5316
BINDING SITE FOR RESIDUE MG D 4401
5
AC5
SOFTWARE
SER A:1017 , GLY A:1018 , VAL A:1019 , GLY A:1020 , LYS A:1021 , THR A:1022 , SER A:1023 , PHE A:1033 , SER A:1034 , ASN A:1035 , TYR A:1037 , THR A:1040 , GLY A:1066 , ASN A:1125 , LYS A:1126 , ASP A:1128 , LEU A:1129 , SER A:1155 , ALA A:1156 , LYS A:1157 , MG A:1401 , HOH A:5002 , HOH A:5017 , HOH A:5033 , HOH A:5079 , HOH A:5314 , HOH A:5456
BINDING SITE FOR RESIDUE GNP A 1400
6
AC6
SOFTWARE
SER B:2017 , GLY B:2018 , VAL B:2019 , GLY B:2020 , LYS B:2021 , THR B:2022 , SER B:2023 , PHE B:2033 , SER B:2034 , ASN B:2035 , TYR B:2037 , THR B:2040 , GLY B:2066 , ASN B:2125 , LYS B:2126 , ASP B:2128 , LEU B:2129 , SER B:2155 , ALA B:2156 , LYS B:2157 , MG B:2401 , HOH B:5006 , HOH B:5020 , HOH B:5028 , HOH B:5156 , HOH B:5315
BINDING SITE FOR RESIDUE GNP B 2400
7
AC7
SOFTWARE
SER C:3017 , GLY C:3018 , VAL C:3019 , GLY C:3020 , LYS C:3021 , THR C:3022 , SER C:3023 , PHE C:3033 , SER C:3034 , ASN C:3035 , TYR C:3037 , THR C:3040 , GLY C:3066 , ASN C:3125 , LYS C:3126 , ASP C:3128 , LEU C:3129 , SER C:3155 , ALA C:3156 , LYS C:3157 , MG C:3401 , HOH C:5001 , HOH C:5009 , HOH C:5013 , HOH C:5032 , HOH C:5219
BINDING SITE FOR RESIDUE GNP C 3400
8
AC8
SOFTWARE
SER D:4017 , GLY D:4018 , VAL D:4019 , GLY D:4020 , LYS D:4021 , THR D:4022 , SER D:4023 , PHE D:4033 , SER D:4034 , ASN D:4035 , TYR D:4037 , THR D:4040 , GLY D:4066 , ASN D:4125 , LYS D:4126 , ASP D:4128 , LEU D:4129 , SER D:4155 , ALA D:4156 , LYS D:4157 , MG D:4401 , HOH D:5003 , HOH D:5024 , HOH D:5027 , HOH D:5069 , HOH D:5177 , HOH D:5316 , HOH D:5425
BINDING SITE FOR RESIDUE GNP D 4400
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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
;
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End label:
Sorry, no Info available
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Exons
(5, 20)
Info
All Exons
Exon 1.1 (A:1007-1018 | B:2006-2018 | C:3007...)
Exon 1.2 (A:1018-1060 | B:2018-2060 | C:3018...)
Exon 1.3 (A:1061-1133 | B:2061-2133 | C:3061...)
Exon 1.4 (A:1134-1176 | B:2134-2176 | C:3134...)
Exon 1.5 (A:1177-1190 | B:2177-2184 | C:3177...)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/-
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
ENSRNOT00000016432
1
ENSRNOE00000116420
chr4:
122220655-122220588
68
RAB7A_RAT
1-18
18
4
A:1007-1018
B:2006-2018
C:3007-3018
D:4007-4018
12
13
12
12
1.2
ENSRNOT00000016432
2
ENSRNOE00000116592
chr4:
122217534-122217408
127
RAB7A_RAT
18-60
43
4
A:1018-1060
B:2018-2060
C:3018-3060
D:4018-4060
43
43
43
43
1.3
ENSRNOT00000016432
3
ENSRNOE00000116782
chr4:
122208992-122208774
219
RAB7A_RAT
61-133
73
4
A:1061-1133
B:2061-2133
C:3061-3133
D:4061-4133
73
73
73
73
1.4
ENSRNOT00000016432
4
ENSRNOE00000116963
chr4:
122208105-122207977
129
RAB7A_RAT
134-176
43
4
A:1134-1176
B:2134-2176
C:3134-3176
D:4134-4176
43
43
43
43
1.5
ENSRNOT00000016432
5
ENSRNOE00000117137
chr4:
122204075-122202697
1379
RAB7A_RAT
177-207
31
4
A:1177-1190
B:2177-2184
C:3177-3184
D:4177-4190
14
8
8
14
[
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]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1vg8a_ (A:)
1b: SCOP_d1vg8b_ (B:)
1c: SCOP_d1vg8c_ (C:)
1d: SCOP_d1vg8d_ (D:)
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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
:
Rab7
(6)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(4)
1a
d1vg8a_
A:
1b
d1vg8b_
B:
1c
d1vg8c_
C:
1d
d1vg8d_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1vg8A00 (A:1007-1190)
1b: CATH_1vg8D00 (D:4007-4190)
1c: CATH_1vg8B00 (B:2006-2184)
1d: CATH_1vg8C00 (C:3007-3184)
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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)
Norway rat (Rattus norvegicus)
(38)
1a
1vg8A00
A:1007-1190
1b
1vg8D00
D:4007-4190
1c
1vg8B00
B:2006-2184
1d
1vg8C00
C:3007-3184
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Ras_1vg8D01 (D:4010-4175)
1b: PFAM_Ras_1vg8D02 (D:4010-4175)
1c: PFAM_Ras_1vg8D03 (D:4010-4175)
1d: PFAM_Ras_1vg8D04 (D:4010-4175)
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Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Rattus norvegicus (Rat)
(6)
1a
Ras-1vg8D01
D:4010-4175
1b
Ras-1vg8D02
D:4010-4175
1c
Ras-1vg8D03
D:4010-4175
1d
Ras-1vg8D04
D:4010-4175
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