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1VG9
Asym. Unit
Info
Asym.Unit (468 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (121 KB)
Biol.Unit 3 (121 KB)
Biol.Unit 4 (120 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURES OF THE REP-1 PROTEIN IN COMPLEX WITH C-TERMINALLY TRUNCATED RAB7 PROTEIN
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
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Rab Prenylation, Post-Translational Modification, Protein Binding/Protein Transport Complex
(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
(4, 16)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
1b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
1c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
1d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33a)
4b: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33b)
4c: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33c)
4d: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
4
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
K
4
Ligand/Ion
POTASSIUM ION
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
P33
4
Ligand/Ion
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
[
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Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR D:22 , ASP D:63 , GDP D:2300 , HOH D:8088 , HOH D:8187 , HOH D:8422 , HOH D:8423
BINDING SITE FOR RESIDUE MG D 2301
02
AC2
SOFTWARE
THR B:22 , GDP B:2302 , HOH B:8006 , HOH B:8152 , HOH B:8358 , HOH B:8359
BINDING SITE FOR RESIDUE MG B 2307
03
AC3
SOFTWARE
GLN B:71 , P33 B:3302 , HOH B:8210
BINDING SITE FOR RESIDUE K B 3303
04
AC4
SOFTWARE
GLN D:71 , P33 D:3304
BINDING SITE FOR RESIDUE K D 3305
05
AC5
SOFTWARE
THR H:22 , ASP H:63 , GDP H:2303 , HOH H:9088 , HOH H:9187 , HOH H:9422 , HOH H:9423
BINDING SITE FOR RESIDUE MG H 2304
06
AC6
SOFTWARE
THR F:22 , GDP F:2305 , HOH F:9006 , HOH F:9152 , HOH F:9358 , HOH F:9359
BINDING SITE FOR RESIDUE MG F 2306
07
AC7
SOFTWARE
GLN F:71 , P33 F:3306 , HOH F:9210
BINDING SITE FOR RESIDUE K F 3307
08
AC8
SOFTWARE
GLN H:71 , P33 H:3308
BINDING SITE FOR RESIDUE K H 3309
09
AC9
SOFTWARE
ASP D:16 , GLY D:18 , VAL D:19 , GLY D:20 , LYS D:21 , THR D:22 , SER D:23 , PHE D:33 , ASN D:125 , LYS D:126 , ASP D:128 , LEU D:129 , SER D:155 , ALA D:156 , LYS D:157 , MG D:2301 , HOH D:8088 , HOH D:8184 , HOH D:8187 , HOH D:8422 , HOH D:8424 , HOH D:8425 , HOH D:8561
BINDING SITE FOR RESIDUE GDP D 2300
10
BC1
SOFTWARE
GLY B:18 , VAL B:19 , GLY B:20 , LYS B:21 , THR B:22 , SER B:23 , PHE B:33 , SER B:34 , ASN B:35 , ASN B:125 , LYS B:126 , ASP B:128 , LEU B:129 , SER B:155 , ALA B:156 , LYS B:157 , MG B:2307 , HOH B:8006 , HOH B:8152 , HOH B:8196 , HOH B:8359 , HOH B:8493 , HOH B:8494 , HOH B:8495
BINDING SITE FOR RESIDUE GDP B 2302
11
BC2
SOFTWARE
ARG A:398 , GLN B:71 , SER B:101 , TRP B:102 , K B:3303 , HOH B:8362
BINDING SITE FOR RESIDUE P33 B 3302
12
BC3
SOFTWARE
ARG C:398 , GLN D:71 , THR D:98 , SER D:101 , TRP D:102 , GLU D:105 , K D:3305
BINDING SITE FOR RESIDUE P33 D 3304
13
BC4
SOFTWARE
GLY H:18 , VAL H:19 , GLY H:20 , LYS H:21 , THR H:22 , SER H:23 , PHE H:33 , ASN H:125 , LYS H:126 , ASP H:128 , LEU H:129 , SER H:155 , ALA H:156 , LYS H:157 , MG H:2304 , HOH H:9088 , HOH H:9184 , HOH H:9187 , HOH H:9422 , HOH H:9424 , HOH H:9425 , HOH H:9577 , HOH H:9594 , HOH H:9595
BINDING SITE FOR RESIDUE GDP H 2303
14
BC5
SOFTWARE
ASP F:16 , GLY F:18 , VAL F:19 , GLY F:20 , LYS F:21 , THR F:22 , SER F:23 , PHE F:33 , SER F:34 , ASN F:35 , ASN F:125 , LYS F:126 , ASP F:128 , LEU F:129 , SER F:155 , ALA F:156 , LYS F:157 , MG F:2306 , HOH F:9006 , HOH F:9152 , HOH F:9163 , HOH F:9196 , HOH F:9359 , HOH F:9493 , HOH F:9494 , HOH F:9495 , HOH F:9497
BINDING SITE FOR RESIDUE GDP F 2305
15
BC6
SOFTWARE
ARG E:398 , GLN F:71 , THR F:98 , SER F:101 , TRP F:102 , GLU F:105 , K F:3307 , HOH F:9362
BINDING SITE FOR RESIDUE P33 F 3306
16
BC7
SOFTWARE
ARG G:398 , GLN H:71 , THR H:98 , SER H:101 , TRP H:102 , GLU H:105 , K H:3309 , HOH H:9573
BINDING SITE FOR RESIDUE P33 H 3308
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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 (B:6-18 | D:6-18 | F:6-18 | H:6-18)
Exon 1.2 (B:18-60 (gaps) | D:18-60 (gaps) | ...)
Exon 1.3 (B:61-133 | D:61-133 | F:61-133 | H...)
Exon 1.4 (B:134-176 | D:134-176 | F:134-176 ...)
Exon 1.5 (B:177-179 | D:177-181 | F:177-178 ...)
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:
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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
B:6-18
D:6-18
F:6-18
H:6-18
13
13
13
13
1.2
ENSRNOT00000016432
2
ENSRNOE00000116592
chr4:
122217534-122217408
127
RAB7A_RAT
18-60
43
4
B:18-60 (gaps)
D:18-60 (gaps)
F:18-60 (gaps)
H:18-60 (gaps)
43
43
43
43
1.3
ENSRNOT00000016432
3
ENSRNOE00000116782
chr4:
122208992-122208774
219
RAB7A_RAT
61-133
73
4
B:61-133
D:61-133
F:61-133
H:61-133
73
73
73
73
1.4
ENSRNOT00000016432
4
ENSRNOE00000116963
chr4:
122208105-122207977
129
RAB7A_RAT
134-176
43
4
B:134-176
D:134-176
F:134-176
H:134-176
43
43
43
43
1.5
ENSRNOT00000016432
5
ENSRNOE00000117137
chr4:
122204075-122202697
1379
RAB7A_RAT
177-207
31
4
B:177-179
D:177-181
F:177-178
H:177-181
3
5
2
5
[
close EXON info
]
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1vg9a2 (A:445-557)
1b: SCOP_d1vg9c2 (C:445-557)
1c: SCOP_d1vg9e2 (E:445-557)
1d: SCOP_d1vg9g2 (G:445-557)
2a: SCOP_d1vg9a1 (A:3-444,A:558-606)
2b: SCOP_d1vg9c1 (C:3-444,C:558-606)
2c: SCOP_d1vg9e1 (E:3-444,E:558-606)
2d: SCOP_d1vg9g1 (G:3-444,G:558-606)
3a: SCOP_d1vg9b_ (B:)
3b: SCOP_d1vg9d_ (D:)
3c: SCOP_d1vg9f_ (F:)
3d: SCOP_d1vg9h_ (H:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-linked reductases, C-terminal domain
(181)
Superfamily
:
FAD-linked reductases, C-terminal domain
(181)
Family
:
GDI-like
(8)
Protein domain
:
Rab escort protein 1
(3)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(3)
1a
d1vg9a2
A:445-557
1b
d1vg9c2
C:445-557
1c
d1vg9e2
E:445-557
1d
d1vg9g2
G:445-557
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
GDI-like N domain
(11)
Protein domain
:
Rab escort protein 1
(3)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(3)
2a
d1vg9a1
A:3-444,A:558-606
2b
d1vg9c1
C:3-444,C:558-606
2c
d1vg9e1
E:3-444,E:558-606
2d
d1vg9g1
G:3-444,G:558-606
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)
3a
d1vg9b_
B:
3b
d1vg9d_
D:
3c
d1vg9f_
F:
3d
d1vg9h_
H:
[
close SCOP info
]
CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_1vg9C02 (C:93-270,C:447-553)
1b: CATH_1vg9G02 (G:93-270,G:447-553)
1c: CATH_1vg9A02 (A:93-270,A:447-553)
1d: CATH_1vg9E02 (E:93-270,E:447-553)
2a: CATH_1vg9D00 (D:6-181)
2b: CATH_1vg9H00 (H:6-181)
2c: CATH_1vg9B00 (B:6-179)
2d: CATH_1vg9F00 (F:6-178)
3a: CATH_1vg9E01 (E:3-92,E:370-446,E:554-601)
3b: CATH_1vg9A01 (A:2-92,A:370-446,A:554-601)
3c: CATH_1vg9C01 (C:3-92,C:370-446,C:554-601)
3d: CATH_1vg9G01 (G:3-92,G:370-446,G:554-601)
4a: CATH_1vg9A03 (A:271-369)
4b: CATH_1vg9C03 (C:271-369)
4c: CATH_1vg9E03 (E:271-369)
4d: CATH_1vg9G03 (G:271-369)
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Classes
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Guanine Nucleotide Dissociation Inhibitor; domain 2
(11)
Homologous Superfamily
:
Guanine Nucleotide Dissociation Inhibitor, domain 2
(11)
Norway rat (Rattus norvegicus)
(3)
1a
1vg9C02
C:93-270,C:447-553
1b
1vg9G02
G:93-270,G:447-553
1c
1vg9A02
A:93-270,A:447-553
1d
1vg9E02
E:93-270,E:447-553
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Norway rat (Rattus norvegicus)
(38)
2a
1vg9D00
D:6-181
2b
1vg9H00
H:6-181
2c
1vg9B00
B:6-179
2d
1vg9F00
F:6-178
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Norway rat (Rattus norvegicus)
(4)
3a
1vg9E01
E:3-92,E:370-446,E:554-601
3b
1vg9A01
A:2-92,A:370-446,A:554-601
3c
1vg9C01
C:3-92,C:370-446,C:554-601
3d
1vg9G01
G:3-92,G:370-446,G:554-601
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Guanine Nucleotide Dissociation Inhibitor; domain 1
(50)
Homologous Superfamily
:
Guanine Nucleotide Dissociation Inhibitor, domain 1
(50)
Norway rat (Rattus norvegicus)
(4)
4a
1vg9A03
A:271-369
4b
1vg9C03
C:271-369
4c
1vg9E03
E:271-369
4d
1vg9G03
G:271-369
[
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]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_GDI_1vg9G01 (G:211-542)
1b: PFAM_GDI_1vg9G02 (G:211-542)
1c: PFAM_GDI_1vg9G03 (G:211-542)
1d: PFAM_GDI_1vg9G04 (G:211-542)
1e: PFAM_GDI_1vg9G05 (G:211-542)
1f: PFAM_GDI_1vg9G06 (G:211-542)
1g: PFAM_GDI_1vg9G07 (G:211-542)
1h: PFAM_GDI_1vg9G08 (G:211-542)
2a: PFAM_Ras_1vg9H01 (H:10-175)
2b: PFAM_Ras_1vg9H02 (H:10-175)
2c: PFAM_Ras_1vg9H03 (H:10-175)
2d: PFAM_Ras_1vg9H04 (H:10-175)
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Clan
:
NADP_Rossmann
(1239)
Family
:
GDI
(6)
Rattus norvegicus (Rat)
(3)
1a
GDI-1vg9G01
G:211-542
1b
GDI-1vg9G02
G:211-542
1c
GDI-1vg9G03
G:211-542
1d
GDI-1vg9G04
G:211-542
1e
GDI-1vg9G05
G:211-542
1f
GDI-1vg9G06
G:211-542
1g
GDI-1vg9G07
G:211-542
1h
GDI-1vg9G08
G:211-542
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Rattus norvegicus (Rat)
(6)
2a
Ras-1vg9H01
H:10-175
2b
Ras-1vg9H02
H:10-175
2c
Ras-1vg9H03
H:10-175
2d
Ras-1vg9H04
H:10-175
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Asym.Unit (468 KB)
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