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1VG9
Biol. Unit 1
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
(2, 2)
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:
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Label:
No.
Name
Count
Type
Full Name
1
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
K
-1
Ligand/Ion
POTASSIUM ION
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
P33
1
Ligand/Ion
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
[
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Sites
(4, 4)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: BC1 (SOFTWARE)
4: BC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
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
2
AC3
SOFTWARE
GLN B:71 , P33 B:3302 , HOH B:8210
BINDING SITE FOR RESIDUE K B 3303
3
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
4
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
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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Exons
(0, 0)
Info
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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:)
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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:
[
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]
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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)
(
)
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)
(
)
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(
)
(
)
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
[
close CATH info
]
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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Clans
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)
(
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(
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(
)
Organisms
(
)
(
)
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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