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1K5D
Biol. Unit 3
Info
Asym.Unit (437 KB)
Biol.Unit 1 (112 KB)
Biol.Unit 2 (112 KB)
Biol.Unit 3 (113 KB)
Biol.Unit 4 (113 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RAN-GPPNHP-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
:
2.70
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, Ground 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
(1, 1)
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
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(2, 2)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
THR G:24 , THR G:42 , GNP G:3250 , HOH G:3253 , HOH G:3254
BINDING SITE FOR RESIDUE MG G 3251
2
AC7
SOFTWARE
GLY G:20 , THR G:21 , GLY G:22 , LYS G:23 , THR G:24 , THR G:25 , GLU G:36 , LYS G:37 , TYR G:39 , THR G:42 , GLY G:68 , GLN G:69 , ASN G:122 , LYS G:123 , ASP G:125 , ILE G:126 , SER G:150 , ALA G:151 , LYS G:152 , MG G:3251 , HOH G:3252 , HOH G:3253 , HOH G:3254
BINDING SITE FOR RESIDUE GNP G 3250
[
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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 G, )
2: VAR_053629 (A145V, chain H, )
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
G
R
95
I
2
UniProt
VAR_053629
A
145
V
RANG_HUMAN
Polymorphism
5746863
H
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 (H: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
-
-
H: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_d1k5db_ (B:)
1b: SCOP_d1k5de_ (E:)
1c: SCOP_d1k5dh_ (H:)
1d: SCOP_d1k5dk_ (K:)
2a: SCOP_d1k5dc_ (C:)
2b: SCOP_d1k5df_ (F:)
2c: SCOP_d1k5di_ (I:)
2d: SCOP_d1k5dl_ (L:)
3a: SCOP_d1k5da_ (A:)
3b: SCOP_d1k5dd_ (D:)
3c: SCOP_d1k5dg_ (G:)
3d: SCOP_d1k5dj_ (J:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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
d1k5db_
B:
1b
d1k5de_
E:
1c
d1k5dh_
H:
1d
d1k5dk_
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
d1k5dc_
C:
2b
d1k5df_
F:
2c
d1k5di_
I:
2d
d1k5dl_
L:
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
d1k5da_
A:
3b
d1k5dd_
D:
3c
d1k5dg_
G:
3d
d1k5dj_
J:
[
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]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1k5dA00 (A:8-213)
1b: CATH_1k5dD00 (D:8-213)
1c: CATH_1k5dG00 (G:8-213)
1d: CATH_1k5dJ00 (J:8-213)
2a: CATH_1k5dC00 (C:2-345)
2b: CATH_1k5dF00 (F:2-345)
2c: CATH_1k5dI00 (I:2-345)
2d: CATH_1k5dL00 (L:2-345)
3a: CATH_1k5dB00 (B:22-167)
3b: CATH_1k5dE00 (E:22-167)
3c: CATH_1k5dH00 (H:22-167)
3d: CATH_1k5dK00 (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
1k5dA00
A:8-213
1b
1k5dD00
D:8-213
1c
1k5dG00
G:8-213
1d
1k5dJ00
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
1k5dC00
C:2-345
2b
1k5dF00
F:2-345
2c
1k5dI00
I:2-345
2d
1k5dL00
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
1k5dB00
B:22-167
3b
1k5dE00
E:22-167
3c
1k5dH00
H:22-167
3d
1k5dK00
K:22-167
[
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_LRR_6_1k5dL01 (L:215-238)
1b: PFAM_LRR_6_1k5dL02 (L:215-238)
1c: PFAM_LRR_6_1k5dL03 (L:215-238)
1d: PFAM_LRR_6_1k5dL04 (L:215-238)
2a: PFAM_Ras_1k5dJ01 (J:12-170)
2b: PFAM_Ras_1k5dJ02 (J:12-170)
2c: PFAM_Ras_1k5dJ03 (J:12-170)
2d: PFAM_Ras_1k5dJ04 (J:12-170)
3a: PFAM_Ran_BP1_1k5dK01 (K:37-161)
3b: PFAM_Ran_BP1_1k5dK02 (K:37-161)
3c: PFAM_Ran_BP1_1k5dK03 (K:37-161)
3d: PFAM_Ran_BP1_1k5dK04 (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_6-1k5dL01
L:215-238
1b
LRR_6-1k5dL02
L:215-238
1c
LRR_6-1k5dL03
L:215-238
1d
LRR_6-1k5dL04
L:215-238
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
2a
Ras-1k5dJ01
J:12-170
2b
Ras-1k5dJ02
J:12-170
2c
Ras-1k5dJ03
J:12-170
2d
Ras-1k5dJ04
J:12-170
Clan
:
PH
(111)
Family
:
Ran_BP1
(9)
Homo sapiens (Human)
(6)
3a
Ran_BP1-1k5dK01
K:37-161
3b
Ran_BP1-1k5dK02
K:37-161
3c
Ran_BP1-1k5dK03
K:37-161
3d
Ran_BP1-1k5dK04
K:37-161
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