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3LSU
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (144 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SOD2 FROM SACCHAROMYCES CEREVISIAE
Authors
:
Y. Sheng, D. Cascio, J. S. Valentine
Date
:
12 Feb 10 (Deposition) - 23 Feb 11 (Release) - 23 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Mn Superoxide Dismutase, Reductive Methylation, Manganese, Metal- Binding, Mitochondrion, Oxidoreductase, Phosphoprotein, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Sheng, D. Cascio, J. S. Valentine
Crystal Structure Of Sod2 From Saccharomyces Cerevisiae
To Be Published
[
close entry info
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Hetero Components
(4, 73)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: N-DIMETHYL-LYSINE (MLYa)
2aa: N-DIMETHYL-LYSINE (MLYaa)
2ab: N-DIMETHYL-LYSINE (MLYab)
2ac: N-DIMETHYL-LYSINE (MLYac)
2ad: N-DIMETHYL-LYSINE (MLYad)
2ae: N-DIMETHYL-LYSINE (MLYae)
2af: N-DIMETHYL-LYSINE (MLYaf)
2ag: N-DIMETHYL-LYSINE (MLYag)
2ah: N-DIMETHYL-LYSINE (MLYah)
2ai: N-DIMETHYL-LYSINE (MLYai)
2aj: N-DIMETHYL-LYSINE (MLYaj)
2ak: N-DIMETHYL-LYSINE (MLYak)
2al: N-DIMETHYL-LYSINE (MLYal)
2am: N-DIMETHYL-LYSINE (MLYam)
2an: N-DIMETHYL-LYSINE (MLYan)
2ao: N-DIMETHYL-LYSINE (MLYao)
2ap: N-DIMETHYL-LYSINE (MLYap)
2aq: N-DIMETHYL-LYSINE (MLYaq)
2ar: N-DIMETHYL-LYSINE (MLYar)
2as: N-DIMETHYL-LYSINE (MLYas)
2at: N-DIMETHYL-LYSINE (MLYat)
2au: N-DIMETHYL-LYSINE (MLYau)
2av: N-DIMETHYL-LYSINE (MLYav)
2aw: N-DIMETHYL-LYSINE (MLYaw)
2ax: N-DIMETHYL-LYSINE (MLYax)
2ay: N-DIMETHYL-LYSINE (MLYay)
2az: N-DIMETHYL-LYSINE (MLYaz)
2b: N-DIMETHYL-LYSINE (MLYb)
2ba: N-DIMETHYL-LYSINE (MLYba)
2bb: N-DIMETHYL-LYSINE (MLYbb)
2bc: N-DIMETHYL-LYSINE (MLYbc)
2bd: N-DIMETHYL-LYSINE (MLYbd)
2be: N-DIMETHYL-LYSINE (MLYbe)
2bf: N-DIMETHYL-LYSINE (MLYbf)
2bg: N-DIMETHYL-LYSINE (MLYbg)
2bh: N-DIMETHYL-LYSINE (MLYbh)
2bi: N-DIMETHYL-LYSINE (MLYbi)
2bj: N-DIMETHYL-LYSINE (MLYbj)
2bk: N-DIMETHYL-LYSINE (MLYbk)
2bl: N-DIMETHYL-LYSINE (MLYbl)
2c: N-DIMETHYL-LYSINE (MLYc)
2d: N-DIMETHYL-LYSINE (MLYd)
2e: N-DIMETHYL-LYSINE (MLYe)
2f: N-DIMETHYL-LYSINE (MLYf)
2g: N-DIMETHYL-LYSINE (MLYg)
2h: N-DIMETHYL-LYSINE (MLYh)
2i: N-DIMETHYL-LYSINE (MLYi)
2j: N-DIMETHYL-LYSINE (MLYj)
2k: N-DIMETHYL-LYSINE (MLYk)
2l: N-DIMETHYL-LYSINE (MLYl)
2m: N-DIMETHYL-LYSINE (MLYm)
2n: N-DIMETHYL-LYSINE (MLYn)
2o: N-DIMETHYL-LYSINE (MLYo)
2p: N-DIMETHYL-LYSINE (MLYp)
2q: N-DIMETHYL-LYSINE (MLYq)
2r: N-DIMETHYL-LYSINE (MLYr)
2s: N-DIMETHYL-LYSINE (MLYs)
2t: N-DIMETHYL-LYSINE (MLYt)
2u: N-DIMETHYL-LYSINE (MLYu)
2v: N-DIMETHYL-LYSINE (MLYv)
2w: N-DIMETHYL-LYSINE (MLYw)
2x: N-DIMETHYL-LYSINE (MLYx)
2y: N-DIMETHYL-LYSINE (MLYy)
2z: N-DIMETHYL-LYSINE (MLYz)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
4a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
MLY
64
Mod. Amino Acid
N-DIMETHYL-LYSINE
3
MN
4
Ligand/Ion
MANGANESE (II) ION
4
NA
1
Ligand/Ion
SODIUM ION
[
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]
Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:26 , HIS A:81 , ASP A:168 , HIS A:172 , HOH A:211
BINDING SITE FOR RESIDUE MN A 208
2
AC2
SOFTWARE
HIS B:26 , HIS B:81 , ASP B:168 , HIS B:172 , HOH B:214
BINDING SITE FOR RESIDUE MN B 208
3
AC3
SOFTWARE
MLY A:8 , GLN A:93 , ASN A:194 , HOH B:230
BINDING SITE FOR RESIDUE GOL B 209
4
AC4
SOFTWARE
HIS C:26 , HIS C:81 , ASP C:168 , HIS C:172 , HOH C:212
BINDING SITE FOR RESIDUE MN C 208
5
AC5
SOFTWARE
GLN C:177 , GLN C:179 , GOL C:210 , HOH C:222 , HOH C:259
BINDING SITE FOR RESIDUE NA C 209
6
AC6
SOFTWARE
GLY A:12 , GLU A:15 , GLN C:177 , TYR C:178 , MLY C:181 , ASP C:184 , NA C:209 , HOH C:259
BINDING SITE FOR RESIDUE GOL C 210
7
AC7
SOFTWARE
HIS D:26 , HIS D:81 , ASP D:168 , HIS D:172 , HOH D:214
BINDING SITE FOR RESIDUE MN D 208
8
AC8
SOFTWARE
GLU B:15 , GLY B:20 , GLN B:21 , TYR D:178 , MLY D:181 , ASP D:184 , HOH D:257
BINDING SITE FOR RESIDUE GOL D 209
9
AC9
SOFTWARE
GLU B:15 , PRO B:16 , ILE B:18 , SER B:19 , GLN B:177 , PRO D:16
BINDING SITE FOR RESIDUE GOL D 210
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: SOD_MN (A:168-175,B:168-175,C:168-175,D:16...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SOD_MN
PS00088
Manganese and iron superoxide dismutases signature.
SODM_YEAST
194-201
4
A:168-175
B:168-175
C:168-175
D:168-175
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Exons
(0, 0)
Info
All Exons
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3lsua1 (A:1-90)
1b: SCOP_d3lsub1 (B:1-90)
1c: SCOP_d3lsuc1 (C:1-90)
1d: SCOP_d3lsud1 (D:1-90)
2a: SCOP_d3lsua2 (A:91-206)
2b: SCOP_d3lsub2 (B:91-207)
2c: SCOP_d3lsuc2 (C:91-206)
2d: SCOP_d3lsud2 (D:91-207)
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)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Long alpha-hairpin
(315)
Superfamily
:
Fe,Mn superoxide dismutase (SOD), N-terminal domain
(122)
Family
:
automated matches
(42)
Protein domain
:
automated matches
(42)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
1a
d3lsua1
A:1-90
1b
d3lsub1
B:1-90
1c
d3lsuc1
C:1-90
1d
d3lsud1
D:1-90
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Fe,Mn superoxide dismutase (SOD), C-terminal domain
(122)
Superfamily
:
Fe,Mn superoxide dismutase (SOD), C-terminal domain
(122)
Family
:
automated matches
(40)
Protein domain
:
automated matches
(40)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
2a
d3lsua2
A:91-206
2b
d3lsub2
B:91-207
2c
d3lsuc2
C:91-206
2d
d3lsud2
D:91-207
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Sod_Fe_C_3lsuD01 (D:96-202)
1b: PFAM_Sod_Fe_C_3lsuD02 (D:96-202)
1c: PFAM_Sod_Fe_C_3lsuD03 (D:96-202)
1d: PFAM_Sod_Fe_C_3lsuD04 (D:96-202)
2a: PFAM_Sod_Fe_N_3lsuD05 (D:1-89)
2b: PFAM_Sod_Fe_N_3lsuD06 (D:1-89)
2c: PFAM_Sod_Fe_N_3lsuD07 (D:1-89)
2d: PFAM_Sod_Fe_N_3lsuD08 (D:1-89)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sod_Fe_C]
(46)
Family
:
Sod_Fe_C
(46)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
1a
Sod_Fe_C-3lsuD01
D:96-202
1b
Sod_Fe_C-3lsuD02
D:96-202
1c
Sod_Fe_C-3lsuD03
D:96-202
1d
Sod_Fe_C-3lsuD04
D:96-202
Clan
:
no clan defined [family: Sod_Fe_N]
(46)
Family
:
Sod_Fe_N
(46)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
2a
Sod_Fe_N-3lsuD05
D:1-89
2b
Sod_Fe_N-3lsuD06
D:1-89
2c
Sod_Fe_N-3lsuD07
D:1-89
2d
Sod_Fe_N-3lsuD08
D:1-89
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