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1K5G
Biol. Unit 1
Info
Asym.Unit (432 KB)
Biol.Unit 1 (111 KB)
Biol.Unit 2 (111 KB)
Biol.Unit 3 (112 KB)
Biol.Unit 4 (112 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RAN-GDP-ALFX-RANBP1-RANGAP COMPLEX
Authors
:
M. J. Seewald, C. Koerner, A. Wittinghofer, I. R. Vetter
Date
:
10 Oct 01 (Deposition) - 13 Feb 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: G,H,I (1x)
Biol. Unit 4: J,K,L (1x)
Keywords
:
Ran, Ranbp1, Rangap, Gap, Signal Transduction, Nuclear Transport, Gtp Hydrolysis, Activation State, Complex (Gtp- Binding/Gtpase Activation), Signaling Protein/Signaling Activator Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Seewald, C. Korner, A. Wittinghofer, I. R. Vetter
Rangap Mediates Gtp Hydrolysis Without An Arginine Finger.
Nature V. 415 662 2002
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: ALUMINUM FLUORIDE (AF3a)
1b: ALUMINUM FLUORIDE (AF3b)
1c: ALUMINUM FLUORIDE (AF3c)
1d: ALUMINUM FLUORIDE (AF3d)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
2c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
2d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AF3
1
Ligand/Ion
ALUMINUM FLUORIDE
2
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:24 , THR A:42 , GDP A:1250 , AF3 A:1252
BINDING SITE FOR RESIDUE MG A 1251
2
AC5
SOFTWARE
GLY A:19 , GLY A:20 , THR A:21 , GLY A:22 , LYS A:23 , THR A:24 , THR A:25 , GLU A:36 , LYS A:37 , TYR A:39 , ASN A:122 , LYS A:123 , ASP A:125 , ILE A:126 , SER A:150 , ALA A:151 , LYS A:152 , MG A:1251 , AF3 A:1252
BINDING SITE FOR RESIDUE GDP A 1250
3
AC6
SOFTWARE
GLY A:19 , GLY A:20 , LYS A:23 , TYR A:39 , ALA A:41 , THR A:42 , GLY A:68 , GLN A:69 , GDP A:1250 , MG A:1251
BINDING SITE FOR RESIDUE AF3 A 1252
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_051900 (R95I, chain A, )
2: VAR_053629 (A145V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051900
R
95
I
RAN_HUMAN
Polymorphism
11546488
A
R
95
I
2
UniProt
VAR_053629
A
145
V
RANG_HUMAN
Polymorphism
5746863
B
A
145
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RANBD1 (B:26-164)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RANBD1
PS50196
Ran binding domain type 1 profile.
RANG_HUMAN
26-164
1
B:26-164
-
-
-
[
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Exons
(0, 0)
Info
All Exons
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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_d1k5gb_ (B:)
1b: SCOP_d1k5ge_ (E:)
1c: SCOP_d1k5gh_ (H:)
1d: SCOP_d1k5gk_ (K:)
2a: SCOP_d1k5gc_ (C:)
2b: SCOP_d1k5gi_ (I:)
2c: SCOP_d1k5gl_ (L:)
2d: SCOP_d1k5gf_ (F:)
3a: SCOP_d1k5ga_ (A:)
3b: SCOP_d1k5gd_ (D:)
3c: SCOP_d1k5gg_ (G:)
3d: SCOP_d1k5gj_ (J:)
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Classes
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(
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Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PH domain-like barrel
(258)
Superfamily
:
PH domain-like
(257)
Family
:
Ran-binding domain
(7)
Protein domain
:
Ran-binding protein 1, Ranbp1
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1k5gb_
B:
1b
d1k5ge_
E:
1c
d1k5gh_
H:
1d
d1k5gk_
K:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(112)
Superfamily
:
RNI-like
(17)
Family
:
Rna1p (RanGAP1), N-terminal domain
(4)
Protein domain
:
Rna1p (RanGAP1), N-terminal domain
(4)
Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]
(4)
2a
d1k5gc_
C:
2b
d1k5gi_
I:
2c
d1k5gl_
L:
2d
d1k5gf_
F:
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
Ran
(37)
Human (Homo sapiens) [TaxId: 9606]
(29)
3a
d1k5ga_
A:
3b
d1k5gd_
D:
3c
d1k5gg_
G:
3d
d1k5gj_
J:
[
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]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1k5gA00 (A:8-213)
1b: CATH_1k5gD00 (D:8-213)
1c: CATH_1k5gG00 (G:8-213)
1d: CATH_1k5gJ00 (J:8-213)
2a: CATH_1k5gC00 (C:2-345)
2b: CATH_1k5gF00 (F:2-345)
2c: CATH_1k5gI00 (I:2-345)
2d: CATH_1k5gL00 (L:2-345)
3a: CATH_1k5gB00 (B:22-167)
3b: CATH_1k5gE00 (E:22-167)
3c: CATH_1k5gH00 (H:22-167)
3d: CATH_1k5gK00 (K:22-167)
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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)
Human (Homo sapiens)
(413)
1a
1k5gA00
A:8-213
1b
1k5gD00
D:8-213
1c
1k5gG00
G:8-213
1d
1k5gJ00
J:8-213
Architecture
:
Alpha-Beta Horseshoe
(92)
Topology
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(73)
Homologous Superfamily
:
Ribonuclease Inhibitor
(73)
Human (Homo sapiens)
(26)
2a
1k5gC00
C:2-345
2b
1k5gF00
F:2-345
2c
1k5gI00
I:2-345
2d
1k5gL00
L:2-345
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
PH-domain like
(150)
Homologous Superfamily
:
Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
(147)
Human (Homo sapiens)
(85)
3a
1k5gB00
B:22-167
3b
1k5gE00
E:22-167
3c
1k5gH00
H:22-167
3d
1k5gK00
K:22-167
[
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_LRR_6_1k5gL01 (L:215-238)
1b: PFAM_LRR_6_1k5gL02 (L:215-238)
1c: PFAM_LRR_6_1k5gL03 (L:215-238)
1d: PFAM_LRR_6_1k5gL04 (L:215-238)
2a: PFAM_Ras_1k5gJ01 (J:12-170)
2b: PFAM_Ras_1k5gJ02 (J:12-170)
2c: PFAM_Ras_1k5gJ03 (J:12-170)
2d: PFAM_Ras_1k5gJ04 (J:12-170)
3a: PFAM_Ran_BP1_1k5gK01 (K:37-161)
3b: PFAM_Ran_BP1_1k5gK02 (K:37-161)
3c: PFAM_Ran_BP1_1k5gK03 (K:37-161)
3d: PFAM_Ran_BP1_1k5gK04 (K:37-161)
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Clans
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Families
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)
Organisms
(
)
(
)
Clan
:
LRR
(77)
Family
:
LRR_6
(24)
Schizosaccharomyces pombe (strain ATCC 38366 / 972) (Fission yeast)
(3)
1a
LRR_6-1k5gL01
L:215-238
1b
LRR_6-1k5gL02
L:215-238
1c
LRR_6-1k5gL03
L:215-238
1d
LRR_6-1k5gL04
L:215-238
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
2a
Ras-1k5gJ01
J:12-170
2b
Ras-1k5gJ02
J:12-170
2c
Ras-1k5gJ03
J:12-170
2d
Ras-1k5gJ04
J:12-170
Clan
:
PH
(111)
Family
:
Ran_BP1
(9)
Homo sapiens (Human)
(6)
3a
Ran_BP1-1k5gK01
K:37-161
3b
Ran_BP1-1k5gK02
K:37-161
3c
Ran_BP1-1k5gK03
K:37-161
3d
Ran_BP1-1k5gK04
K:37-161
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Asym.Unit (432 KB)
Header - Asym.Unit
Biol.Unit 1 (111 KB)
Header - Biol.Unit 1
Biol.Unit 2 (111 KB)
Header - Biol.Unit 2
Biol.Unit 3 (112 KB)
Header - Biol.Unit 3
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