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3GQF
Biol. Unit 2
Info
Asym.Unit (149 KB)
Biol.Unit 1 (51 KB)
Biol.Unit 2 (50 KB)
Biol.Unit 3 (51 KB)
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Title
:
STRUCTURAL AND BIOPHYSICAL PROPERTIES OF THE PATHOGENIC SOD1 VARIANT H46R/H48Q
Authors
:
D. D. Winkler, J. P. Schuermann, P. J. Hart
Date
:
24 Mar 09 (Deposition) - 07 Apr 09 (Release) - 16 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Human Cu-Zn Superoxide Dismutase, Superoxide Acceptor, Familial Amyotrophic Lateral Sclerosis Mutant, Acetylation, Amyotrophic Lateral Sclerosis, Antioxidant, Copper, Cytoplasm, Disease Mutation, Disulfide Bond, Metal-Binding, Oxidoreductase, Phosphoprotein, Ubl Conjugation, Zinc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. D. Winkler, J. P. Schuermann, X. Cao, S. P. Holloway, D. R. Borchelt, M. C. Carroll, J. B. Proescher, V. C. Culotta, P. J. Hart
Structural And Biophysical Properties Of The Pathogenic Sod1 Variant H46R/H48Q.
Biochemistry V. 48 3436 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(4, 4)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
HIS C:63 , HIS C:71 , HIS C:80 , ASP C:83
BINDING SITE FOR RESIDUE ZN C 155
2
AC6
SOFTWARE
ASN C:26 , SER C:102 , HOH C:488 , HOH C:494 , HOH C:495 , HOH C:496
BINDING SITE FOR RESIDUE CA C 154
3
AC7
SOFTWARE
HIS D:63 , HIS D:71 , HIS D:80 , ASP D:83
BINDING SITE FOR RESIDUE ZN D 155
4
AC8
SOFTWARE
ASN D:26 , SER D:102 , HOH D:489 , HOH D:497 , HOH D:498
BINDING SITE FOR RESIDUE CA D 154
[
close Site info
]
SAPs(SNPs)/Variants
(78, 156)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_013518 (A4S, chain C/D, )
02: VAR_007130 (A4T, chain C/D, )
03: VAR_007131 (A4V, chain C/D, )
04: VAR_008717 (C6F, chain C/D, )
05: VAR_007132 (V7E, chain C/D, )
06: VAR_013519 (L8Q, chain C/D, )
07: VAR_013520 (L8V, chain C/D, )
08: VAR_013521 (G12R, chain C/D, )
09: VAR_013522 (V14G, chain C/D, )
10: VAR_007133 (V14M, chain C/D, )
11: VAR_007134 (G16S, chain C/D, )
12: VAR_045876 (F20C, chain C/D, )
13: VAR_013523 (E21G, chain C/D, )
14: VAR_007135 (E21K, chain C/D, )
15: VAR_045877 (Q22L, chain C/D, )
16: VAR_007136 (G37R, chain C/D, )
17: VAR_013524 (L38R, chain C/D, )
18: VAR_007137 (L38V, chain C/D, )
19: VAR_007139 (G41D, chain C/D, )
20: VAR_007138 (G41S, chain C/D, )
21: VAR_007140 (H43R, chain C/D, )
22: VAR_013525 (F45C, chain C/D, )
23: VAR_007141 (R46R, chain C/D, )
24: VAR_007142 (Q48Q, chain C/D, )
25: VAR_045878 (Q48R, chain C/D, )
26: VAR_013526 (E49K, chain C/D, )
27: VAR_045879 (T54R, chain C/D, )
28: VAR_013527 (N65S, chain C/D, )
29: VAR_065560 (L67P, chain C/D, )
30: VAR_013528 (L67R, chain C/D, )
31: VAR_008718 (G72S, chain C/D, )
32: VAR_013529 (D76Y, chain C/D, )
33: VAR_016874 (H80A, chain C/D, )
34: VAR_013530 (L84F, chain C/D, )
35: VAR_007143 (L84V, chain C/D, )
36: VAR_007144 (G85R, chain C/D, )
37: VAR_013531 (N86S, chain C/D, )
38: VAR_045880 (V87A, chain C/D, )
39: VAR_045881 (A89T, chain C/D, )
40: VAR_013532 (A89V, chain C/D, )
41: VAR_007145 (D90A, chain C/D, )
42: VAR_013533 (D90V, chain C/D, )
43: VAR_007146 (G93A, chain C/D, )
44: VAR_007147 (G93C, chain C/D, )
45: VAR_007148 (G93D, chain C/D, )
46: VAR_007149 (G93R, chain C/D, )
47: VAR_008719 (G93V, chain C/D, )
48: VAR_065194 (A95G, chain C/D, )
49: VAR_045882 (V97M, chain C/D, )
50: VAR_007150 (E100G, chain C/D, )
51: VAR_013534 (E100K, chain C/D, )
52: VAR_007151 (D101G, chain C/D, )
53: VAR_007152 (D101N, chain C/D, )
54: VAR_008720 (I104F, chain C/D, )
55: VAR_013535 (S105L, chain C/D, )
56: VAR_007153 (L106V, chain C/D, )
57: VAR_013536 (G108V, chain C/D, )
58: VAR_013537 (I112M, chain C/D, )
59: VAR_007154 (I112T, chain C/D, )
60: VAR_007155 (I113T, chain C/D, )
61: VAR_013538 (G114A, chain C/D, )
62: VAR_007156 (R115G, chain C/D, )
63: VAR_045883 (V118L, chain C/D, )
64: VAR_045884 (D124G, chain C/D, )
65: VAR_008722 (D124V, chain C/D, )
66: VAR_007157 (D125H, chain C/D, )
67: VAR_013539 (L126S, chain C/D, )
68: VAR_007158 (S134N, chain C/D, )
69: VAR_007159 (N139K, chain C/D, )
70: VAR_007160 (L144F, chain C/D, )
71: VAR_008724 (L144S, chain C/D, )
72: VAR_008725 (A145T, chain C/D, )
73: VAR_013540 (C146R, chain C/D, )
74: VAR_045885 (G147R, chain C/D, )
75: VAR_007161 (V148G, chain C/D, )
76: VAR_007162 (V148I, chain C/D, )
77: VAR_007163 (I149T, chain C/D, )
78: VAR_007164 (I151T, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_013518
A
5
S
SODC_HUMAN
Disease (ALS1)
---
C/D
A
4
S
02
UniProt
VAR_007130
A
5
T
SODC_HUMAN
Disease (ALS1)
---
C/D
A
4
T
03
UniProt
VAR_007131
A
5
V
SODC_HUMAN
Disease (ALS1)
---
C/D
A
4
V
04
UniProt
VAR_008717
C
7
F
SODC_HUMAN
Disease (ALS1)
---
C/D
C
6
F
05
UniProt
VAR_007132
V
8
E
SODC_HUMAN
Disease (ALS1)
---
C/D
V
7
E
06
UniProt
VAR_013519
L
9
Q
SODC_HUMAN
Disease (ALS1)
---
C/D
L
8
Q
07
UniProt
VAR_013520
L
9
V
SODC_HUMAN
Disease (ALS1)
---
C/D
L
8
V
08
UniProt
VAR_013521
G
13
R
SODC_HUMAN
Disease (ALS1)
---
C/D
G
12
R
09
UniProt
VAR_013522
V
15
G
SODC_HUMAN
Disease (ALS1)
---
C/D
V
14
G
10
UniProt
VAR_007133
V
15
M
SODC_HUMAN
Disease (ALS1)
---
C/D
V
14
M
11
UniProt
VAR_007134
G
17
S
SODC_HUMAN
Disease (ALS1)
---
C/D
G
16
S
12
UniProt
VAR_045876
F
21
C
SODC_HUMAN
Disease (ALS1)
---
C/D
F
20
C
13
UniProt
VAR_013523
E
22
G
SODC_HUMAN
Disease (ALS1)
---
C/D
E
21
G
14
UniProt
VAR_007135
E
22
K
SODC_HUMAN
Disease (ALS1)
---
C/D
E
21
K
15
UniProt
VAR_045877
Q
23
L
SODC_HUMAN
Disease (ALS1)
---
C/D
Q
22
L
16
UniProt
VAR_007136
G
38
R
SODC_HUMAN
Disease (ALS1)
---
C/D
G
37
R
17
UniProt
VAR_013524
L
39
R
SODC_HUMAN
Disease (ALS1)
---
C/D
L
38
R
18
UniProt
VAR_007137
L
39
V
SODC_HUMAN
Disease (ALS1)
---
C/D
L
38
V
19
UniProt
VAR_007139
G
42
D
SODC_HUMAN
Disease (ALS1)
---
C/D
G
41
D
20
UniProt
VAR_007138
G
42
S
SODC_HUMAN
Disease (ALS1)
---
C/D
G
41
S
21
UniProt
VAR_007140
H
44
R
SODC_HUMAN
Disease (ALS1)
---
C/D
H
43
R
22
UniProt
VAR_013525
F
46
C
SODC_HUMAN
Disease (ALS1)
---
C/D
F
45
C
23
UniProt
VAR_007141
H
47
R
SODC_HUMAN
Disease (ALS1)
---
C/D
R
46
R
24
UniProt
VAR_007142
H
49
Q
SODC_HUMAN
Disease (ALS1)
---
C/D
Q
48
Q
25
UniProt
VAR_045878
H
49
R
SODC_HUMAN
Disease (ALS1)
---
C/D
Q
48
R
26
UniProt
VAR_013526
E
50
K
SODC_HUMAN
Disease (ALS1)
---
C/D
E
49
K
27
UniProt
VAR_045879
T
55
R
SODC_HUMAN
Disease (ALS1)
---
C/D
T
54
R
28
UniProt
VAR_013527
N
66
S
SODC_HUMAN
Disease (ALS1)
---
C/D
N
65
S
29
UniProt
VAR_065560
L
68
P
SODC_HUMAN
Disease (ALS1)
---
C/D
L
67
P
30
UniProt
VAR_013528
L
68
R
SODC_HUMAN
Disease (ALS1)
---
C/D
L
67
R
31
UniProt
VAR_008718
G
73
S
SODC_HUMAN
Disease (ALS1)
---
C/D
G
72
S
32
UniProt
VAR_013529
D
77
Y
SODC_HUMAN
Disease (ALS1)
---
C/D
D
76
Y
33
UniProt
VAR_016874
H
81
A
SODC_HUMAN
Disease (ALS1)
---
C/D
H
80
A
34
UniProt
VAR_013530
L
85
F
SODC_HUMAN
Disease (ALS1)
---
C/D
L
84
F
35
UniProt
VAR_007143
L
85
V
SODC_HUMAN
Disease (ALS1)
---
C/D
L
84
V
36
UniProt
VAR_007144
G
86
R
SODC_HUMAN
Disease (ALS1)
---
C/D
G
85
R
37
UniProt
VAR_013531
N
87
S
SODC_HUMAN
Disease (ALS1)
11556620
C/D
N
86
S
38
UniProt
VAR_045880
V
88
A
SODC_HUMAN
Disease (ALS1)
---
C/D
V
87
A
39
UniProt
VAR_045881
A
90
T
SODC_HUMAN
Disease (ALS1)
---
C/D
A
89
T
40
UniProt
VAR_013532
A
90
V
SODC_HUMAN
Disease (ALS1)
---
C/D
A
89
V
41
UniProt
VAR_007145
D
91
A
SODC_HUMAN
Disease (ALS1)
80265967
C/D
D
90
A
42
UniProt
VAR_013533
D
91
V
SODC_HUMAN
Disease (ALS1)
---
C/D
D
90
V
43
UniProt
VAR_007146
G
94
A
SODC_HUMAN
Disease (ALS1)
---
C/D
G
93
A
44
UniProt
VAR_007147
G
94
C
SODC_HUMAN
Disease (ALS1)
---
C/D
G
93
C
45
UniProt
VAR_007148
G
94
D
SODC_HUMAN
Disease (ALS1)
---
C/D
G
93
D
46
UniProt
VAR_007149
G
94
R
SODC_HUMAN
Disease (ALS1)
---
C/D
G
93
R
47
UniProt
VAR_008719
G
94
V
SODC_HUMAN
Disease (ALS1)
---
C/D
G
93
V
48
UniProt
VAR_065194
A
96
G
SODC_HUMAN
Disease (ALS1)
---
C/D
A
95
G
49
UniProt
VAR_045882
V
98
M
SODC_HUMAN
Disease (ALS1)
---
C/D
V
97
M
50
UniProt
VAR_007150
E
101
G
SODC_HUMAN
Disease (ALS1)
---
C/D
E
100
G
51
UniProt
VAR_013534
E
101
K
SODC_HUMAN
Disease (ALS1)
---
C/D
E
100
K
52
UniProt
VAR_007151
D
102
G
SODC_HUMAN
Disease (ALS1)
---
C/D
D
101
G
53
UniProt
VAR_007152
D
102
N
SODC_HUMAN
Disease (ALS1)
---
C/D
D
101
N
54
UniProt
VAR_008720
I
105
F
SODC_HUMAN
Disease (ALS1)
---
C/D
I
104
F
55
UniProt
VAR_013535
S
106
L
SODC_HUMAN
Disease (ALS1)
---
C/D
S
105
L
56
UniProt
VAR_007153
L
107
V
SODC_HUMAN
Disease (ALS1)
---
C/D
L
106
V
57
UniProt
VAR_013536
G
109
V
SODC_HUMAN
Disease (ALS1)
---
C/D
G
108
V
58
UniProt
VAR_013537
I
113
M
SODC_HUMAN
Disease (ALS1)
---
C/D
I
112
M
59
UniProt
VAR_007154
I
113
T
SODC_HUMAN
Disease (ALS1)
---
C/D
I
112
T
60
UniProt
VAR_007155
I
114
T
SODC_HUMAN
Disease (ALS1)
---
C/D
I
113
T
61
UniProt
VAR_013538
G
115
A
SODC_HUMAN
Disease (ALS1)
---
C/D
G
114
A
62
UniProt
VAR_007156
R
116
G
SODC_HUMAN
Disease (ALS1)
---
C/D
R
115
G
63
UniProt
VAR_045883
V
119
L
SODC_HUMAN
Disease (ALS1)
---
C/D
V
118
L
64
UniProt
VAR_045884
D
125
G
SODC_HUMAN
Disease (ALS1)
---
C/D
D
124
G
65
UniProt
VAR_008722
D
125
V
SODC_HUMAN
Disease (ALS1)
---
C/D
D
124
V
66
UniProt
VAR_007157
D
126
H
SODC_HUMAN
Disease (ALS1)
---
C/D
D
125
H
67
UniProt
VAR_013539
L
127
S
SODC_HUMAN
Disease (ALS1)
---
C/D
L
126
S
68
UniProt
VAR_007158
S
135
N
SODC_HUMAN
Disease (ALS1)
---
C/D
S
134
N
69
UniProt
VAR_007159
N
140
K
SODC_HUMAN
Disease (ALS1)
---
C/D
N
139
K
70
UniProt
VAR_007160
L
145
F
SODC_HUMAN
Disease (ALS1)
---
C/D
L
144
F
71
UniProt
VAR_008724
L
145
S
SODC_HUMAN
Disease (ALS1)
---
C/D
L
144
S
72
UniProt
VAR_008725
A
146
T
SODC_HUMAN
Disease (ALS1)
---
C/D
A
145
T
73
UniProt
VAR_013540
C
147
R
SODC_HUMAN
Disease (ALS1)
---
C/D
C
146
R
74
UniProt
VAR_045885
G
148
R
SODC_HUMAN
Disease (ALS1)
---
C/D
G
147
R
75
UniProt
VAR_007161
V
149
G
SODC_HUMAN
Disease (ALS1)
---
C/D
V
148
G
76
UniProt
VAR_007162
V
149
I
SODC_HUMAN
Disease (ALS1)
---
C/D
V
148
I
77
UniProt
VAR_007163
I
150
T
SODC_HUMAN
Disease (ALS1)
---
C/D
I
149
T
78
UniProt
VAR_007164
I
152
T
SODC_HUMAN
Disease (ALS1)
---
C/D
I
151
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: SOD_CU_ZN_1 (C:44-54,D:44-54)
2: SOD_CU_ZN_2 (C:138-149,D:138-149)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SOD_CU_ZN_1
PS00087
Copper/Zinc superoxide dismutase signature 1.
SODC_HUMAN
45-55
2
-
-
C:44-54
D:44-54
-
-
2
SOD_CU_ZN_2
PS00332
Copper/Zinc superoxide dismutase signature 2.
SODC_HUMAN
139-150
2
-
-
C:138-149
D:138-149
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3gqfa_ (A:)
1b: SCOP_d3gqfb_ (B:)
1c: SCOP_d3gqfc_ (C:)
1d: SCOP_d3gqfd_ (D:)
1e: SCOP_d3gqfe_ (E:)
1f: SCOP_d3gqff_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Cu,Zn superoxide dismutase-like
(165)
Family
:
Cu,Zn superoxide dismutase-like
(158)
Protein domain
:
Cu,Zn superoxide dismutase, SOD
(134)
Human (Homo sapiens) [TaxId: 9606]
(69)
1a
d3gqfa_
A:
1b
d3gqfb_
B:
1c
d3gqfc_
C:
1d
d3gqfd_
D:
1e
d3gqfe_
E:
1f
d3gqff_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3gqfA00 (A:1-153)
1b: CATH_3gqfB00 (B:1-153)
1c: CATH_3gqfC00 (C:1-153)
1d: CATH_3gqfD00 (D:1-153)
1e: CATH_3gqfE00 (E:1-153)
1f: CATH_3gqfF00 (F:1-153)
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Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.200, no name defined]
(125)
Human (Homo sapiens)
(52)
1a
3gqfA00
A:1-153
1b
3gqfB00
B:1-153
1c
3gqfC00
C:1-153
1d
3gqfD00
D:1-153
1e
3gqfE00
E:1-153
1f
3gqfF00
F:1-153
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