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3K9S
Asym. Unit
Info
Asym.Unit (275 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (136 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PEROXIDE-BOUND MANGANESE SUPEROXIDE DISMUTASE.
Authors
:
J. C. Porta, A. Vahedi-Faridi, G. E. O. Borgstahl
Date
:
16 Oct 09 (Deposition) - 12 May 10 (Release) - 18 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Manganese Superoxide Dismutase, Peroxide-Bound, Manganese, Metal- Binding, Oxidoreductase
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Reference
:
J. Porta, A. Vahedi-Faridi, G. E. Borgstahl
Structural Analysis Of Peroxide-Soaked Mnsod Crystals Reveals Side-On Binding Of Peroxide To Active-Site Manganese.
J. Mol. Biol. V. 399 377 2010
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
2a: HYDROGEN PEROXIDE (PEOa)
2b: HYDROGEN PEROXIDE (PEOb)
2c: HYDROGEN PEROXIDE (PEOc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
4
Ligand/Ion
MANGANESE (II) ION
2
PEO
3
Ligand/Ion
HYDROGEN PEROXIDE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:26 , HIS A:81 , ASP A:167 , HIS A:171 , HOH A:207 , HOH A:208
BINDING SITE FOR RESIDUE MN A 206
2
AC2
SOFTWARE
HIS B:26 , HIS B:81 , ASP B:167 , HIS B:171 , PEO B:207 , HOH B:208
BINDING SITE FOR RESIDUE MN B 206
3
AC3
SOFTWARE
TYR B:34 , HIS B:81 , GLN B:146 , ASP B:167 , TRP B:169 , HIS B:171 , MN B:206 , HOH B:208
BINDING SITE FOR RESIDUE PEO B 207
4
AC4
SOFTWARE
HIS C:26 , HIS C:81 , ASP C:167 , HIS C:171 , PEO C:207 , HOH C:208 , HOH C:209
BINDING SITE FOR RESIDUE MN C 206
5
AC5
SOFTWARE
HIS C:81 , TRP C:128 , GLN C:146 , ASP C:167 , TRP C:169 , HIS C:171 , MN C:206 , HOH C:208 , HOH C:209
BINDING SITE FOR RESIDUE PEO C 207
6
AC6
SOFTWARE
HIS D:26 , HIS D:81 , ASP D:167 , HIS D:171 , PEO D:208 , HOH D:209
BINDING SITE FOR RESIDUE MN D 206
7
AC7
SOFTWARE
TYR D:34 , HIS D:81 , GLN D:146 , ASP D:167 , TRP D:169 , HIS D:171 , MN D:206 , HOH D:209
BINDING SITE FOR RESIDUE PEO D 208
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SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_SODM_ECOLI_001 (M164L, chain A/B/C/D, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_SODM_ECOLI_001
*
M
165
L
SODM_ECOLI
---
---
A/B/C/D
M
164
L
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: SOD_MN (A:167-174,B:167-174,C:167-174,D:16...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SOD_MN
PS00088
Manganese and iron superoxide dismutases signature.
SODM_ECOLI
168-175
4
A:167-174
B:167-174
C:167-174
D:167-174
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Exons
(0, 0)
Info
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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_d3k9sa1 (A:1-90)
1b: SCOP_d3k9sb1 (B:1-90)
1c: SCOP_d3k9sc1 (C:1-90)
1d: SCOP_d3k9sd1 (D:1-90)
2a: SCOP_d3k9sa2 (A:91-205)
2b: SCOP_d3k9sb2 (B:91-205)
2c: SCOP_d3k9sc2 (C:91-205)
2d: SCOP_d3k9sd2 (D:91-205)
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Protein Domains
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Organisms
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Class
:
All alpha proteins
(14657)
Fold
:
Long alpha-hairpin
(315)
Superfamily
:
Fe,Mn superoxide dismutase (SOD), N-terminal domain
(122)
Family
:
Fe,Mn superoxide dismutase (SOD), N-terminal domain
(80)
Protein domain
:
Mn superoxide dismutase (MnSOD)
(47)
Escherichia coli K-12 [TaxId: 83333]
(1)
1a
d3k9sa1
A:1-90
1b
d3k9sb1
B:1-90
1c
d3k9sc1
C:1-90
1d
d3k9sd1
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
:
Fe,Mn superoxide dismutase (SOD), C-terminal domain
(82)
Protein domain
:
Mn superoxide dismutase (MnSOD)
(47)
Escherichia coli K-12 [TaxId: 83333]
(1)
2a
d3k9sa2
A:91-205
2b
d3k9sb2
B:91-205
2c
d3k9sc2
C:91-205
2d
d3k9sd2
D:91-205
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Sod_Fe_C_3k9sD01 (D:92-201)
1b: PFAM_Sod_Fe_C_3k9sD02 (D:92-201)
1c: PFAM_Sod_Fe_C_3k9sD03 (D:92-201)
1d: PFAM_Sod_Fe_C_3k9sD04 (D:92-201)
2a: PFAM_Sod_Fe_N_3k9sD05 (D:1-89)
2b: PFAM_Sod_Fe_N_3k9sD06 (D:1-89)
2c: PFAM_Sod_Fe_N_3k9sD07 (D:1-89)
2d: PFAM_Sod_Fe_N_3k9sD08 (D:1-89)
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Clan
:
no clan defined [family: Sod_Fe_C]
(46)
Family
:
Sod_Fe_C
(46)
Escherichia coli (strain K12)
(7)
1a
Sod_Fe_C-3k9sD01
D:92-201
1b
Sod_Fe_C-3k9sD02
D:92-201
1c
Sod_Fe_C-3k9sD03
D:92-201
1d
Sod_Fe_C-3k9sD04
D:92-201
Clan
:
no clan defined [family: Sod_Fe_N]
(46)
Family
:
Sod_Fe_N
(46)
Escherichia coli (strain K12)
(7)
2a
Sod_Fe_N-3k9sD05
D:1-89
2b
Sod_Fe_N-3k9sD06
D:1-89
2c
Sod_Fe_N-3k9sD07
D:1-89
2d
Sod_Fe_N-3k9sD08
D:1-89
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Asym.Unit (275 KB)
Header - Asym.Unit
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