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3KH4
Biol. Unit 3
Info
Asym.Unit (295 KB)
Biol.Unit 1 (98 KB)
Biol.Unit 2 (99 KB)
Biol.Unit 3 (99 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CU/ZN SUPEROXIDE DISMUTASE RECOMBINANTLY PRODUCED IN LEISHMANIA TARANTOLAE; P6522 CRYSTAL FORM CONTAINING 6 CHAINS IN THE ASYMMETRIC UNIT
Authors
:
E. M. Gazdag, W. Blankenfeldt
Date
:
30 Oct 09 (Deposition) - 11 Aug 10 (Release) - 01 Sep 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
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
:
Eukaryotic Expression, Leishmania Tarantolae, Amyotrophic Lateral Sclerosis, Antioxidant, Disease Mutation, Disulfide Bond, Metal- Binding, Neurodegeneration, Oxidoreductase, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. M. Gazdag, I. C. Cirstea, R. Breitling, J. Lukes, W. Blankenfeldt, K. Alexandrov
Purification And Crystallization Of Human Cu/Zn Superoxide Dismutase Recombinantly Produced In The Protozoan Leishmani Tarentolae.
Acta Crystallogr. , Sect. F V. 66 871 2010
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
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: AC9 (SOFTWARE)
2: BC1 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC9
SOFTWARE
HIS E:46 , HIS E:48 , HIS E:63 , HIS E:120
BINDING SITE FOR RESIDUE CU E 154
2
BC1
SOFTWARE
HIS E:63 , HIS E:71 , HIS E:80 , ASP E:83 , LYS E:136
BINDING SITE FOR RESIDUE ZN E 155
3
BC2
SOFTWARE
HIS F:46 , HIS F:48 , HIS F:63 , HIS F:120
BINDING SITE FOR RESIDUE CU F 154
4
BC3
SOFTWARE
HIS F:63 , HIS F:71 , HIS F:80 , ASP F:83 , LYS F:136
BINDING SITE FOR RESIDUE ZN F 155
[
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 E/F, )
02: VAR_007130 (A4T, chain E/F, )
03: VAR_007131 (A4V, chain E/F, )
04: VAR_008717 (C6F, chain E/F, )
05: VAR_007132 (V7E, chain E/F, )
06: VAR_013519 (L8Q, chain E/F, )
07: VAR_013520 (L8V, chain E/F, )
08: VAR_013521 (G12R, chain E/F, )
09: VAR_013522 (V14G, chain E/F, )
10: VAR_007133 (V14M, chain E/F, )
11: VAR_007134 (G16S, chain E/F, )
12: VAR_045876 (F20C, chain E/F, )
13: VAR_013523 (E21G, chain E/F, )
14: VAR_007135 (E21K, chain E/F, )
15: VAR_045877 (Q22L, chain E/F, )
16: VAR_007136 (G37R, chain E/F, )
17: VAR_013524 (L38R, chain E/F, )
18: VAR_007137 (L38V, chain E/F, )
19: VAR_007139 (G41D, chain E/F, )
20: VAR_007138 (G41S, chain E/F, )
21: VAR_007140 (H43R, chain E/F, )
22: VAR_013525 (F45C, chain E/F, )
23: VAR_007141 (H46R, chain E/F, )
24: VAR_007142 (H48Q, chain E/F, )
25: VAR_045878 (H48R, chain E/F, )
26: VAR_013526 (E49K, chain E/F, )
27: VAR_045879 (T54R, chain E/F, )
28: VAR_013527 (N65S, chain E/F, )
29: VAR_065560 (L67P, chain E/F, )
30: VAR_013528 (L67R, chain E/F, )
31: VAR_008718 (G72S, chain E/F, )
32: VAR_013529 (D76Y, chain E/F, )
33: VAR_016874 (H80A, chain E/F, )
34: VAR_013530 (L84F, chain E/F, )
35: VAR_007143 (L84V, chain E/F, )
36: VAR_007144 (G85R, chain E/F, )
37: VAR_013531 (N86S, chain E/F, )
38: VAR_045880 (V87A, chain E/F, )
39: VAR_045881 (A89T, chain E/F, )
40: VAR_013532 (A89V, chain E/F, )
41: VAR_007145 (D90A, chain E/F, )
42: VAR_013533 (D90V, chain E/F, )
43: VAR_007146 (G93A, chain E/F, )
44: VAR_007147 (G93C, chain E/F, )
45: VAR_007148 (G93D, chain E/F, )
46: VAR_007149 (G93R, chain E/F, )
47: VAR_008719 (G93V, chain E/F, )
48: VAR_065194 (A95G, chain E/F, )
49: VAR_045882 (V97M, chain E/F, )
50: VAR_007150 (E100G, chain E/F, )
51: VAR_013534 (E100K, chain E/F, )
52: VAR_007151 (D101G, chain E/F, )
53: VAR_007152 (D101N, chain E/F, )
54: VAR_008720 (I104F, chain E/F, )
55: VAR_013535 (S105L, chain E/F, )
56: VAR_007153 (L106V, chain E/F, )
57: VAR_013536 (G108V, chain E/F, )
58: VAR_013537 (I112M, chain E/F, )
59: VAR_007154 (I112T, chain E/F, )
60: VAR_007155 (I113T, chain E/F, )
61: VAR_013538 (G114A, chain E/F, )
62: VAR_007156 (R115G, chain E/F, )
63: VAR_045883 (V118L, chain E/F, )
64: VAR_045884 (D124G, chain E/F, )
65: VAR_008722 (D124V, chain E/F, )
66: VAR_007157 (D125H, chain E/F, )
67: VAR_013539 (L126S, chain E/F, )
68: VAR_007158 (S134N, chain E/F, )
69: VAR_007159 (N139K, chain E/F, )
70: VAR_007160 (L144F, chain E/F, )
71: VAR_008724 (L144S, chain E/F, )
72: VAR_008725 (A145T, chain E/F, )
73: VAR_013540 (C146R, chain E/F, )
74: VAR_045885 (G147R, chain E/F, )
75: VAR_007161 (V148G, chain E/F, )
76: VAR_007162 (V148I, chain E/F, )
77: VAR_007163 (I149T, chain E/F, )
78: VAR_007164 (I151T, chain E/F, )
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)
---
E/F
A
4
S
02
UniProt
VAR_007130
A
5
T
SODC_HUMAN
Disease (ALS1)
---
E/F
A
4
T
03
UniProt
VAR_007131
A
5
V
SODC_HUMAN
Disease (ALS1)
---
E/F
A
4
V
04
UniProt
VAR_008717
C
7
F
SODC_HUMAN
Disease (ALS1)
---
E/F
C
6
F
05
UniProt
VAR_007132
V
8
E
SODC_HUMAN
Disease (ALS1)
---
E/F
V
7
E
06
UniProt
VAR_013519
L
9
Q
SODC_HUMAN
Disease (ALS1)
---
E/F
L
8
Q
07
UniProt
VAR_013520
L
9
V
SODC_HUMAN
Disease (ALS1)
---
E/F
L
8
V
08
UniProt
VAR_013521
G
13
R
SODC_HUMAN
Disease (ALS1)
---
E/F
G
12
R
09
UniProt
VAR_013522
V
15
G
SODC_HUMAN
Disease (ALS1)
---
E/F
V
14
G
10
UniProt
VAR_007133
V
15
M
SODC_HUMAN
Disease (ALS1)
---
E/F
V
14
M
11
UniProt
VAR_007134
G
17
S
SODC_HUMAN
Disease (ALS1)
---
E/F
G
16
S
12
UniProt
VAR_045876
F
21
C
SODC_HUMAN
Disease (ALS1)
---
E/F
F
20
C
13
UniProt
VAR_013523
E
22
G
SODC_HUMAN
Disease (ALS1)
---
E/F
E
21
G
14
UniProt
VAR_007135
E
22
K
SODC_HUMAN
Disease (ALS1)
---
E/F
E
21
K
15
UniProt
VAR_045877
Q
23
L
SODC_HUMAN
Disease (ALS1)
---
E/F
Q
22
L
16
UniProt
VAR_007136
G
38
R
SODC_HUMAN
Disease (ALS1)
---
E/F
G
37
R
17
UniProt
VAR_013524
L
39
R
SODC_HUMAN
Disease (ALS1)
---
E/F
L
38
R
18
UniProt
VAR_007137
L
39
V
SODC_HUMAN
Disease (ALS1)
---
E/F
L
38
V
19
UniProt
VAR_007139
G
42
D
SODC_HUMAN
Disease (ALS1)
---
E/F
G
41
D
20
UniProt
VAR_007138
G
42
S
SODC_HUMAN
Disease (ALS1)
---
E/F
G
41
S
21
UniProt
VAR_007140
H
44
R
SODC_HUMAN
Disease (ALS1)
---
E/F
H
43
R
22
UniProt
VAR_013525
F
46
C
SODC_HUMAN
Disease (ALS1)
---
E/F
F
45
C
23
UniProt
VAR_007141
H
47
R
SODC_HUMAN
Disease (ALS1)
---
E/F
H
46
R
24
UniProt
VAR_007142
H
49
Q
SODC_HUMAN
Disease (ALS1)
---
E/F
H
48
Q
25
UniProt
VAR_045878
H
49
R
SODC_HUMAN
Disease (ALS1)
---
E/F
H
48
R
26
UniProt
VAR_013526
E
50
K
SODC_HUMAN
Disease (ALS1)
---
E/F
E
49
K
27
UniProt
VAR_045879
T
55
R
SODC_HUMAN
Disease (ALS1)
---
E/F
T
54
R
28
UniProt
VAR_013527
N
66
S
SODC_HUMAN
Disease (ALS1)
---
E/F
N
65
S
29
UniProt
VAR_065560
L
68
P
SODC_HUMAN
Disease (ALS1)
---
E/F
L
67
P
30
UniProt
VAR_013528
L
68
R
SODC_HUMAN
Disease (ALS1)
---
E/F
L
67
R
31
UniProt
VAR_008718
G
73
S
SODC_HUMAN
Disease (ALS1)
---
E/F
G
72
S
32
UniProt
VAR_013529
D
77
Y
SODC_HUMAN
Disease (ALS1)
---
E/F
D
76
Y
33
UniProt
VAR_016874
H
81
A
SODC_HUMAN
Disease (ALS1)
---
E/F
H
80
A
34
UniProt
VAR_013530
L
85
F
SODC_HUMAN
Disease (ALS1)
---
E/F
L
84
F
35
UniProt
VAR_007143
L
85
V
SODC_HUMAN
Disease (ALS1)
---
E/F
L
84
V
36
UniProt
VAR_007144
G
86
R
SODC_HUMAN
Disease (ALS1)
---
E/F
G
85
R
37
UniProt
VAR_013531
N
87
S
SODC_HUMAN
Disease (ALS1)
11556620
E/F
N
86
S
38
UniProt
VAR_045880
V
88
A
SODC_HUMAN
Disease (ALS1)
---
E/F
V
87
A
39
UniProt
VAR_045881
A
90
T
SODC_HUMAN
Disease (ALS1)
---
E/F
A
89
T
40
UniProt
VAR_013532
A
90
V
SODC_HUMAN
Disease (ALS1)
---
E/F
A
89
V
41
UniProt
VAR_007145
D
91
A
SODC_HUMAN
Disease (ALS1)
80265967
E/F
D
90
A
42
UniProt
VAR_013533
D
91
V
SODC_HUMAN
Disease (ALS1)
---
E/F
D
90
V
43
UniProt
VAR_007146
G
94
A
SODC_HUMAN
Disease (ALS1)
---
E/F
G
93
A
44
UniProt
VAR_007147
G
94
C
SODC_HUMAN
Disease (ALS1)
---
E/F
G
93
C
45
UniProt
VAR_007148
G
94
D
SODC_HUMAN
Disease (ALS1)
---
E/F
G
93
D
46
UniProt
VAR_007149
G
94
R
SODC_HUMAN
Disease (ALS1)
---
E/F
G
93
R
47
UniProt
VAR_008719
G
94
V
SODC_HUMAN
Disease (ALS1)
---
E/F
G
93
V
48
UniProt
VAR_065194
A
96
G
SODC_HUMAN
Disease (ALS1)
---
E/F
A
95
G
49
UniProt
VAR_045882
V
98
M
SODC_HUMAN
Disease (ALS1)
---
E/F
V
97
M
50
UniProt
VAR_007150
E
101
G
SODC_HUMAN
Disease (ALS1)
---
E/F
E
100
G
51
UniProt
VAR_013534
E
101
K
SODC_HUMAN
Disease (ALS1)
---
E/F
E
100
K
52
UniProt
VAR_007151
D
102
G
SODC_HUMAN
Disease (ALS1)
---
E/F
D
101
G
53
UniProt
VAR_007152
D
102
N
SODC_HUMAN
Disease (ALS1)
---
E/F
D
101
N
54
UniProt
VAR_008720
I
105
F
SODC_HUMAN
Disease (ALS1)
---
E/F
I
104
F
55
UniProt
VAR_013535
S
106
L
SODC_HUMAN
Disease (ALS1)
---
E/F
S
105
L
56
UniProt
VAR_007153
L
107
V
SODC_HUMAN
Disease (ALS1)
---
E/F
L
106
V
57
UniProt
VAR_013536
G
109
V
SODC_HUMAN
Disease (ALS1)
---
E/F
G
108
V
58
UniProt
VAR_013537
I
113
M
SODC_HUMAN
Disease (ALS1)
---
E/F
I
112
M
59
UniProt
VAR_007154
I
113
T
SODC_HUMAN
Disease (ALS1)
---
E/F
I
112
T
60
UniProt
VAR_007155
I
114
T
SODC_HUMAN
Disease (ALS1)
---
E/F
I
113
T
61
UniProt
VAR_013538
G
115
A
SODC_HUMAN
Disease (ALS1)
---
E/F
G
114
A
62
UniProt
VAR_007156
R
116
G
SODC_HUMAN
Disease (ALS1)
---
E/F
R
115
G
63
UniProt
VAR_045883
V
119
L
SODC_HUMAN
Disease (ALS1)
---
E/F
V
118
L
64
UniProt
VAR_045884
D
125
G
SODC_HUMAN
Disease (ALS1)
---
E/F
D
124
G
65
UniProt
VAR_008722
D
125
V
SODC_HUMAN
Disease (ALS1)
---
E/F
D
124
V
66
UniProt
VAR_007157
D
126
H
SODC_HUMAN
Disease (ALS1)
---
E/F
D
125
H
67
UniProt
VAR_013539
L
127
S
SODC_HUMAN
Disease (ALS1)
---
E/F
L
126
S
68
UniProt
VAR_007158
S
135
N
SODC_HUMAN
Disease (ALS1)
---
E/F
S
134
N
69
UniProt
VAR_007159
N
140
K
SODC_HUMAN
Disease (ALS1)
---
E/F
N
139
K
70
UniProt
VAR_007160
L
145
F
SODC_HUMAN
Disease (ALS1)
---
E/F
L
144
F
71
UniProt
VAR_008724
L
145
S
SODC_HUMAN
Disease (ALS1)
---
E/F
L
144
S
72
UniProt
VAR_008725
A
146
T
SODC_HUMAN
Disease (ALS1)
---
E/F
A
145
T
73
UniProt
VAR_013540
C
147
R
SODC_HUMAN
Disease (ALS1)
---
E/F
C
146
R
74
UniProt
VAR_045885
G
148
R
SODC_HUMAN
Disease (ALS1)
---
E/F
G
147
R
75
UniProt
VAR_007161
V
149
G
SODC_HUMAN
Disease (ALS1)
---
E/F
V
148
G
76
UniProt
VAR_007162
V
149
I
SODC_HUMAN
Disease (ALS1)
---
E/F
V
148
I
77
UniProt
VAR_007163
I
150
T
SODC_HUMAN
Disease (ALS1)
---
E/F
I
149
T
78
UniProt
VAR_007164
I
152
T
SODC_HUMAN
Disease (ALS1)
---
E/F
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 (E:44-54,F:44-54)
2: SOD_CU_ZN_2 (E:138-149,F: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
-
-
-
-
E:44-54
F:44-54
2
SOD_CU_ZN_2
PS00332
Copper/Zinc superoxide dismutase signature 2.
SODC_HUMAN
139-150
2
-
-
-
-
E:138-149
F: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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Sod_Cu_3kh4F01 (F:4-149)
1b: PFAM_Sod_Cu_3kh4F02 (F:4-149)
1c: PFAM_Sod_Cu_3kh4F03 (F:4-149)
1d: PFAM_Sod_Cu_3kh4F04 (F:4-149)
1e: PFAM_Sod_Cu_3kh4F05 (F:4-149)
1f: PFAM_Sod_Cu_3kh4F06 (F:4-149)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sod_Cu]
(71)
Family
:
Sod_Cu
(71)
Homo sapiens (Human)
(34)
1a
Sod_Cu-3kh4F01
F:4-149
1b
Sod_Cu-3kh4F02
F:4-149
1c
Sod_Cu-3kh4F03
F:4-149
1d
Sod_Cu-3kh4F04
F:4-149
1e
Sod_Cu-3kh4F05
F:4-149
1f
Sod_Cu-3kh4F06
F:4-149
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
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background
color...
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RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
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Asym.Unit (295 KB)
Header - Asym.Unit
Biol.Unit 1 (98 KB)
Header - Biol.Unit 1
Biol.Unit 2 (99 KB)
Header - Biol.Unit 2
Biol.Unit 3 (99 KB)
Header - Biol.Unit 3
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