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1K5D
Asym. Unit
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
)
[
close entry info
]
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
[
close Hetero Component info
]
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:24 , THR A:42 , GNP A:1250 , HOH A:1253 , HOH A:1254
BINDING SITE FOR RESIDUE MG A 1251
2
AC2
SOFTWARE
THR D:24 , THR D:42 , GNP D:2250 , HOH D:2253 , HOH D:2254
BINDING SITE FOR RESIDUE MG D 2251
3
AC3
SOFTWARE
THR G:24 , THR G:42 , GNP G:3250 , HOH G:3253 , HOH G:3254
BINDING SITE FOR RESIDUE MG G 3251
4
AC4
SOFTWARE
THR J:24 , THR J:42 , GNP J:4250 , HOH J:4253 , HOH J:4254
BINDING SITE FOR RESIDUE MG J 4251
5
AC5
SOFTWARE
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 , THR A:42 , GLY A:68 , GLN A:69 , ASN A:122 , LYS A:123 , ASP A:125 , ILE A:126 , SER A:150 , ALA A:151 , LYS A:152 , MG A:1251 , HOH A:1252 , HOH A:1253 , HOH A:1254 , HOH A:1257
BINDING SITE FOR RESIDUE GNP A 1250
6
AC6
SOFTWARE
GLY D:20 , THR D:21 , GLY D:22 , LYS D:23 , THR D:24 , THR D:25 , GLU D:36 , LYS D:37 , TYR D:39 , ALA D:41 , THR D:42 , GLY D:68 , GLN D:69 , ASN D:122 , LYS D:123 , ASP D:125 , ILE D:126 , SER D:150 , ALA D:151 , LYS D:152 , MG D:2251 , HOH D:2252 , HOH D:2253 , HOH D:2254 , HOH D:2263
BINDING SITE FOR RESIDUE GNP D 2250
7
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
8
AC8
SOFTWARE
GLY J:20 , THR J:21 , GLY J:22 , LYS J:23 , THR J:24 , THR J:25 , GLU J:36 , LYS J:37 , TYR J:39 , THR J:42 , GLY J:68 , GLN J:69 , ASN J:122 , LYS J:123 , ASP J:125 , ILE J:126 , SER J:150 , ALA J:151 , LYS J:152 , MG J:4251 , HOH J:4252 , HOH J:4253 , HOH J:4254 , HOH J:4280
BINDING SITE FOR RESIDUE GNP J 4250
[
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]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_051900 (R95I, chain A/D/G/J, )
2: VAR_053629 (A145V, chain B/E/H/K, )
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/D/G/J
R
95
I
2
UniProt
VAR_053629
A
145
V
RANG_HUMAN
Polymorphism
5746863
B/E/H/K
A
145
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: RANBD1 (B:26-164,E:26-164,H:26-164,K:26-16...)
;
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
4
B:26-164
E:26-164
H:26-164
K:26-164
[
close PROSITE info
]
Exons
(9, 36)
Info
All Exons
Exon 1.4a (B:22-51 | E:22-51 | H:22-51 | K:22...)
Exon 1.5b (B:51-104 | E:51-104 | H:51-104 | K...)
Exon 1.6b (B:104-147 | E:104-147 | H:104-147 ...)
Exon 1.7a (B:147-167 | E:147-167 | H:147-167 ...)
Exon 2.2a (A:8-32 | D:8-32 | G:8-32 | J:8-32)
Exon 2.2d (A:33-61 | D:33-61 | G:33-61 | J:33...)
Exon 2.3 (A:61-103 | D:61-103 | G:61-103 | J...)
Exon 2.5b (A:103-165 | D:103-165 | G:103-165 ...)
Exon 2.6c (A:166-213 | D:166-213 | G:166-213 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2d/1.4a
02: Boundary 1.4a/1.5b
03: Boundary 1.5b/1.6b
04: Boundary 1.6b/1.7a
05: Boundary 1.7a/1.7e
06: Boundary -/2.2a
07: Boundary 2.2a/2.2d
08: Boundary 2.2d/2.3
09: Boundary 2.3/2.5b
10: Boundary 2.5b/2.6c
11: Boundary 2.6c/2.7c
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
1.2d
ENST00000331821
2d
ENSE00001953373
chr22:
20105071-20105187
117
RANG_HUMAN
1-5
5
0
-
-
1.4a
ENST00000331821
4a
ENSE00001636910
chr22:
20106536-20106672
137
RANG_HUMAN
6-51
46
4
B:22-51
E:22-51
H:22-51
K:22-51
30
30
30
30
1.5b
ENST00000331821
5b
ENSE00002146443
chr22:
20109787-20109944
158
RANG_HUMAN
51-104
54
4
B:51-104
E:51-104
H:51-104
K:51-104
54
54
54
54
1.6b
ENST00000331821
6b
ENSE00001700647
chr22:
20112831-20112959
129
RANG_HUMAN
104-147
44
4
B:104-147
E:104-147
H:104-147
K:104-147
44
44
44
44
1.7a
ENST00000331821
7a
ENSE00000650881
chr22:
20113826-20113891
66
RANG_HUMAN
147-169
23
4
B:147-167
E:147-167
H:147-167
K:147-167
21
21
21
21
1.7e
ENST00000331821
7e
ENSE00001320805
chr22:
20114475-20114704
230
RANG_HUMAN
169-201
33
0
-
-
2.2a
ENST00000392369
2a
ENSE00001511608
chr12:
131356783-131357174
392
RAN_HUMAN
1-32
32
4
A:8-32
D:8-32
G:8-32
J:8-32
25
25
25
25
2.2d
ENST00000392369
2d
ENSE00000903701
chr12:
131357381-131357465
85
RAN_HUMAN
33-61
29
4
A:33-61
D:33-61
G:33-61
J:33-61
29
29
29
29
2.3
ENST00000392369
3
ENSE00000903703
chr12:
131357548-131357673
126
RAN_HUMAN
61-103
43
4
A:61-103
D:61-103
G:61-103
J:61-103
43
43
43
43
2.5b
ENST00000392369
5b
ENSE00000903705
chr12:
131359091-131359278
188
RAN_HUMAN
103-165
63
4
A:103-165
D:103-165
G:103-165
J:103-165
63
63
63
63
2.6c
ENST00000392369
6c
ENSE00000903707
chr12:
131360157-131360327
171
RAN_HUMAN
166-222
57
4
A:166-213
D:166-213
G:166-213
J:166-213
48
48
48
48
2.7c
ENST00000392369
7c
ENSE00001511600
chr12:
131360427-131360826
400
RAN_HUMAN
223-236
14
0
-
-
[
close EXON info
]
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:)
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)
(
)
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(
)
(
)
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:
[
close SCOP info
]
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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Organisms
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)
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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