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1SDY
Asym. Unit
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Asym.Unit (108 KB)
Biol.Unit 1 (102 KB)
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(1)
Title
:
STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE
Authors
:
K. Djinovic, G. Gatti, A. Coda, L. Antolini, G. Pelosi, A. Desideri, M. Falconi, F. Marmocchi, G. Rotilio, M. Bolognesi
Date
:
14 Jun 91 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase(Superoxide Acceptor)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Djinovic, G. Gatti, A. Coda, L. Antolini, G. Pelosi, A. Desideri, M. Falconi, F. Marmocchi, G. Rolilio, M. Bolognesi
Structure Solution And Molecular Dynamics Refinement Of The Yeast Cu, Zn Enzyme Superoxide Dismutase.
Acta Crystallogr. , Sect. B V. 47 918 1991
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
4
Ligand/Ion
COPPER (II) ION
2
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(12, 12)
Info
All Sites
01: A (UNKNOWN)
02: AC1 (SOFTWARE)
03: AC2 (SOFTWARE)
04: AC3 (SOFTWARE)
05: AC4 (SOFTWARE)
06: AC5 (SOFTWARE)
07: AC6 (SOFTWARE)
08: AC7 (SOFTWARE)
09: AC8 (SOFTWARE)
10: B (UNKNOWN)
11: C (UNKNOWN)
12: D (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
A
UNKNOWN
HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118 , HIS A:69 , HIS A:78 , ASP A:81 , CU A:152 , ZN A:153
NULL
02
AC1
SOFTWARE
HIS A:44 , HIS A:46 , HIS A:61 , HIS A:118 , HOH A:154
BINDING SITE FOR RESIDUE CU A 152
03
AC2
SOFTWARE
HIS A:61 , HIS A:69 , HIS A:78 , ASP A:81
BINDING SITE FOR RESIDUE ZN A 153
04
AC3
SOFTWARE
HIS B:44 , HIS B:46 , HIS B:61 , HIS B:118 , HOH B:154
BINDING SITE FOR RESIDUE CU B 152
05
AC4
SOFTWARE
HIS B:61 , HIS B:69 , HIS B:78 , ASP B:81
BINDING SITE FOR RESIDUE ZN B 153
06
AC5
SOFTWARE
HIS C:44 , HIS C:46 , HIS C:61 , HIS C:118 , HOH C:154
BINDING SITE FOR RESIDUE CU C 152
07
AC6
SOFTWARE
HIS C:61 , HIS C:69 , HIS C:78 , ASP C:81
BINDING SITE FOR RESIDUE ZN C 153
08
AC7
SOFTWARE
HIS D:44 , HIS D:46 , HIS D:61 , HIS D:118 , HOH D:154
BINDING SITE FOR RESIDUE CU D 152
09
AC8
SOFTWARE
HIS D:61 , HIS D:69 , HIS D:78 , ASP D:81
BINDING SITE FOR RESIDUE ZN D 153
10
B
UNKNOWN
HIS B:44 , HIS B:46 , HIS B:61 , HIS B:118 , HIS B:69 , HIS B:78 , ASP B:81 , CU B:152 , ZN B:153
NULL
11
C
UNKNOWN
HIS C:44 , HIS C:46 , HIS C:61 , HIS C:118 , HIS C:69 , HIS C:78 , ASP C:81 , CU C:152 , ZN C:153
NULL
12
D
UNKNOWN
HIS D:44 , HIS D:46 , HIS D:61 , HIS D:118 , HIS D:69 , HIS D:78 , ASP D:81 , CU D:152 , ZN D:153
NULL
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: SOD_CU_ZN_1 (A:42-52,B:42-52,C:42-52,D:42-52)
2: SOD_CU_ZN_2 (A:136-147,B:136-147,C:136-147,D:13...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SOD_CU_ZN_1
PS00087
Copper/Zinc superoxide dismutase signature 1.
SODC_YEAST
45-55
4
A:42-52
B:42-52
C:42-52
D:42-52
2
SOD_CU_ZN_2
PS00332
Copper/Zinc superoxide dismutase signature 2.
SODC_YEAST
139-150
4
A:136-147
B:136-147
C:136-147
D:136-147
[
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]
Exons
(1, 4)
Info
All Exons
Exon 1.1 (A:2-151 | B:2-151 | C:2-151 | D:2-...)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YJR104C
1
YJR104C.1
X:623002-622538
465
SODC_YEAST
1-154
154
4
A:2-151
B:2-151
C:2-151
D:2-151
153
153
153
153
[
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]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1sdya_ (A:)
1b: SCOP_d1sdyb_ (B:)
1c: SCOP_d1sdyc_ (C:)
1d: SCOP_d1sdyd_ (D:)
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)
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)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(12)
1a
d1sdya_
A:
1b
d1sdyb_
B:
1c
d1sdyc_
C:
1d
d1sdyd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1sdyA00 (A:2-151)
1b: CATH_1sdyB00 (B:2-151)
1c: CATH_1sdyC00 (C:2-151)
1d: CATH_1sdyD00 (D:2-151)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.200, no name defined]
(125)
Baker's yeast (Saccharomyces cerevisiae)
(13)
1a
1sdyA00
A:2-151
1b
1sdyB00
B:2-151
1c
1sdyC00
C:2-151
1d
1sdyD00
D:2-151
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Sod_Cu_1sdyD01 (D:4-147)
1b: PFAM_Sod_Cu_1sdyD02 (D:4-147)
1c: PFAM_Sod_Cu_1sdyD03 (D:4-147)
1d: PFAM_Sod_Cu_1sdyD04 (D:4-147)
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)
Clan
:
no clan defined [family: Sod_Cu]
(71)
Family
:
Sod_Cu
(71)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
1a
Sod_Cu-1sdyD01
D:4-147
1b
Sod_Cu-1sdyD02
D:4-147
1c
Sod_Cu-1sdyD03
D:4-147
1d
Sod_Cu-1sdyD04
D:4-147
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Asymmetric Unit 1
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