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3Q5E
Asym. Unit
Info
Asym.Unit (556 KB)
Biol.Unit 1 (146 KB)
Biol.Unit 2 (145 KB)
Biol.Unit 3 (136 KB)
Biol.Unit 4 (136 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN ATLASTIN-1 (RESIDUES 1-447) BOUND TO GDP, CRYSTAL FORM 2
Authors
:
L. J. Byrnes, H. Sondermann
Date
:
28 Dec 10 (Deposition) - 19 Jan 11 (Release) - 20 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.01
Chains
:
Asym. Unit : A,C,E,G
Biol. Unit 1: A (1x)
Biol. Unit 2: C (1x)
Biol. Unit 3: E (1x)
Biol. Unit 4: G (1x)
Keywords
:
G Protein, Gtpase, Gdp/Gtp Binding, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. J. Byrnes, H. Sondermann
Structural Basis For The Nucleotide-Dependent Dimerization Of The Large G Protein Atlastin-1/Spg3A.
Proc. Natl. Acad. Sci. Usa V. 108 2216 2011
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Hetero Components
(2, 8)
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: 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
GDP
4
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
MG
4
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
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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
ARG A:77 , LYS A:78 , GLY A:79 , LYS A:80 , SER A:81 , PHE A:82 , GLU A:117 , GLN A:148 , ARG A:217 , ASP A:218 , PRO A:272 , VAL A:276 , ALA A:277 , ASN A:279 , PRO A:280 , MG A:448
BINDING SITE FOR RESIDUE GDP A 3850
2
AC2
SOFTWARE
SER A:81 , ASP A:146 , GLN A:148 , GDP A:3850
BINDING SITE FOR RESIDUE MG A 448
3
AC3
SOFTWARE
ARG C:77 , LYS C:78 , GLY C:79 , LYS C:80 , SER C:81 , PHE C:82 , ARG C:217 , ASP C:218 , PRO C:272 , VAL C:276 , ASN C:279 , PRO C:280
BINDING SITE FOR RESIDUE GDP C 3850
4
AC4
SOFTWARE
SER C:81
BINDING SITE FOR RESIDUE MG C 448
5
AC5
SOFTWARE
PHE E:76 , ARG E:77 , LYS E:78 , GLY E:79 , LYS E:80 , SER E:81 , PHE E:82 , GLN E:148 , ARG E:217 , ASP E:218 , PRO E:272 , VAL E:276 , ALA E:277 , ASN E:279 , PRO E:280
BINDING SITE FOR RESIDUE GDP E 3850
6
AC6
SOFTWARE
SER E:81
BINDING SITE FOR RESIDUE MG E 448
7
AC7
SOFTWARE
ALA G:75 , ARG G:77 , LYS G:78 , GLY G:79 , LYS G:80 , SER G:81 , PHE G:82 , GLN G:148 , ARG G:217 , ASP G:218 , HIS G:271 , PRO G:272 , VAL G:276 , ASN G:279
BINDING SITE FOR RESIDUE GDP G 3850
8
AC8
SOFTWARE
SER G:81 , GLN G:124 , ASP G:146 , GLN G:148
BINDING SITE FOR RESIDUE MG G 448
[
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SAPs(SNPs)/Variants
(21, 73)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_058963 (D43E, chain A/C/E/G, )
02: VAR_065508 (E66Q, chain A/C/E/G, )
03: VAR_071874 (R118Q, chain A/C, )
04: VAR_067655 (Q154E, chain A/C, )
05: VAR_065509 (L157W, chain A/C, )
06: VAR_019446 (A161P, chain A/C/E/G, )
07: VAR_058964 (F193C, chain A/C/E/G, )
08: VAR_067656 (Y196C, chain A/C/E/G, )
09: VAR_017146 (R217Q, chain A/C/E/G, )
10: VAR_017147 (R239C, chain A/C/E/G, )
11: VAR_019447 (H247P, chain A/C, )
12: VAR_067657 (V253I, chain A/C/E/G, )
13: VAR_017148 (H258R, chain A/C/E/G, )
14: VAR_017149 (S259Y, chain A/C/E/G, )
15: VAR_065510 (N355K, chain A/C/E/G, )
16: VAR_065511 (M408V, chain A/C/E/G, )
17: VAR_067658 (F413V, chain A/C/E/G, )
18: VAR_071708 (R415Q, chain A/C/E/G, )
19: VAR_065512 (R415W, chain A/C/E/G, )
20: VAR_071709 (R416C, chain A/C/E/G, )
21: VAR_067659 (N440T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_058963
D
43
E
ATLA1_HUMAN
Polymorphism
17850684
A/C/E/G
D
43
E
02
UniProt
VAR_065508
E
66
Q
ATLA1_HUMAN
Disease (HSN1D)
---
A/C/E/G
E
66
Q
03
UniProt
VAR_071874
R
118
Q
ATLA1_HUMAN
Disease (SPG3)
---
A/C
R
118
Q
04
UniProt
VAR_067655
Q
154
E
ATLA1_HUMAN
Disease (SPG3)
---
A/C
Q
154
E
05
UniProt
VAR_065509
L
157
W
ATLA1_HUMAN
Disease (SPG3)
---
A/C
L
157
W
06
UniProt
VAR_019446
A
161
P
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
A
161
P
07
UniProt
VAR_058964
F
193
C
ATLA1_HUMAN
Polymorphism
17850683
A/C/E/G
F
193
C
08
UniProt
VAR_067656
Y
196
C
ATLA1_HUMAN
Unclassified
---
A/C/E/G
Y
196
C
09
UniProt
VAR_017146
R
217
Q
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
R
217
Q
10
UniProt
VAR_017147
R
239
C
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
R
239
C
11
UniProt
VAR_019447
H
247
P
ATLA1_HUMAN
Disease (SPG3)
---
A/C
H
247
P
12
UniProt
VAR_067657
V
253
I
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
V
253
I
13
UniProt
VAR_017148
H
258
R
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
H
258
R
14
UniProt
VAR_017149
S
259
Y
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
S
259
Y
15
UniProt
VAR_065510
N
355
K
ATLA1_HUMAN
Disease (HSN1D)
---
A/C/E/G
N
355
K
16
UniProt
VAR_065511
M
408
V
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
M
408
V
17
UniProt
VAR_067658
F
413
V
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
F
413
V
18
UniProt
VAR_071708
R
415
Q
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
R
415
Q
19
UniProt
VAR_065512
R
415
W
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
R
415
W
20
UniProt
VAR_071709
R
416
C
ATLA1_HUMAN
Disease (SPG3)
---
A/C/E/G
R
416
C
21
UniProt
VAR_067659
N
440
T
ATLA1_HUMAN
Disease (SPG3)
---
A
N
440
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: G_GB1_RHD3 (A:64-309,C:64-309,E:64-309,G:64-30...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G_GB1_RHD3
PS51715
GB1/RHD3-type guanine nucleotide-binding (G) domain profile.
ATLA1_HUMAN
64-309
4
A:64-309
C:64-309
E:64-309
G:64-309
[
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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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GBP_3q5eG01 (G:43-314)
1b: PFAM_GBP_3q5eG02 (G:43-314)
1c: PFAM_GBP_3q5eG03 (G:43-314)
1d: PFAM_GBP_3q5eG04 (G:43-314)
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)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
GBP
(4)
Homo sapiens (Human)
(4)
1a
GBP-3q5eG01
G:43-314
1b
GBP-3q5eG02
G:43-314
1c
GBP-3q5eG03
G:43-314
1d
GBP-3q5eG04
G:43-314
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