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1X3S
Asym. Unit
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Asym.Unit (39 KB)
Biol.Unit 1 (35 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN RAB18 IN COMPLEX WITH GPPNHP
Authors
:
M. Kukimoto-Niino, K. Murayama, L. Chen, Z. J. Liu, B. C. Wang, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
10 May 05 (Deposition) - 10 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.32
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Gtpase, Rab, Gnp, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Endocytosis/Exocytosis Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kukimoto-Niino, K. Murayama, L. Chen, Z. J. Liu, B. C. Wang, M. Shirouzu, S. Yokoyama
Crystal Structure Of Human Rab18 In Complex With Gppnhp
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
2a: MAGNESIUM ION (MGa)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
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
3
MSE
2
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:22 , THR A:40 , GNP A:300 , HOH A:301 , HOH A:303
BINDING SITE FOR RESIDUE MG A 200
2
AC2
SOFTWARE
SER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , SER A:22 , SER A:23 , PHE A:33 , ASP A:34 , PRO A:35 , ALA A:39 , THR A:40 , GLY A:66 , ASN A:122 , LYS A:123 , ASP A:125 , LYS A:126 , SER A:151 , ALA A:152 , LYS A:153 , MG A:200 , HOH A:301 , HOH A:303 , HOH A:309 , HOH A:319 , HOH A:330 , HOH A:357 , HOH A:360 , HOH A:361
BINDING SITE FOR RESIDUE GNP A 300
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066495 (L24Q, chain A, )
2: VAR_051713 (N113S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066495
L
24
Q
RAB18_HUMAN
Disease (WARBM3)
---
A
L
24
Q
2
UniProt
VAR_051713
N
113
S
RAB18_HUMAN
Polymorphism
12268932
A
N
113
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RAB (A:2-178)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAB
PS51419
small GTPase Rab1 family profile.
RAB18_HUMAN
2-199
1
A:2-178
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Exons
(7, 7)
Info
All Exons
Exon 1.1a (A:2-23)
Exon 1.4a (A:23-42)
Exon 1.6 (A:42-62)
Exon 1.8 (A:63-87)
Exon 1.9 (A:87-126)
Exon 1.10 (A:127-149)
Exon 1.11e (A:149-178)
View:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.4a
3: Boundary 1.4a/1.6
4: Boundary 1.6/1.8
5: Boundary 1.8/1.9
6: Boundary 1.9/1.10
7: Boundary 1.10/1.11e
8: Boundary 1.11e/-
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
1.1a
ENST00000356940
1a
ENSE00001907702
chr10:
27793197-27793366
170
RAB18_HUMAN
1-23
23
1
A:2-23
22
1.4a
ENST00000356940
4a
ENSE00001700205
chr10:
27798804-27798859
56
RAB18_HUMAN
23-42
20
1
A:23-42
20
1.6
ENST00000356940
6
ENSE00000985386
chr10:
27815757-27815818
62
RAB18_HUMAN
42-62
21
1
A:42-62
21
1.8
ENST00000356940
8
ENSE00000985387
chr10:
27821436-27821508
73
RAB18_HUMAN
63-87
25
1
A:63-87
25
1.9
ENST00000356940
9
ENSE00000985388
chr10:
27822664-27822782
119
RAB18_HUMAN
87-126
40
1
A:87-126
40
1.10
ENST00000356940
10
ENSE00000985389
chr10:
27822857-27822923
67
RAB18_HUMAN
127-149
23
1
A:127-149
23
1.11e
ENST00000356940
11e
ENSE00001415399
chr10:
27826805-27829092
2288
RAB18_HUMAN
149-206
58
1
A:149-178
30
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1x3sa1 (A:2-178)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
Rab18
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1x3sa1
A:2-178
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1x3sA00 (A:2-178)
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)
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
1x3sA00
A:2-178
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Ras_1x3sA01 (A:10-171)
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Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
1a
Ras-1x3sA01
A:10-171
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Asymmetric Unit 1
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