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Title :   THREE-DIMENSIONAL STRUCTURE OF CU,ZN-SUPEROXIDE DISMUTASE FROM SPINACH AT 2.0 ANGSTROMS RESOLUTION

Authors :   Y. Kitagawa, Y. Katsube

Date :   15 Apr 93 (Deposition) - 31 Jan 94 (Release) - 22 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Superoxide Acceptor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kitagawa, N. Tanaka, Y. Hata, M. Kusunoki, G. P. Lee, Y. Katsube, K. Asada, S. Aibara, Y. Morita
Three-Dimensional Structure Of Cu, Zn-Superoxide Dismutase From Spinach At 2. 0 A Resolution.
J. Biochem. (Tokyo) V. 109 477 1991
PubMed-ID: 1880134
(for further references see the PDB file header)

Molecule 1 - COPPER,ZINC SUPEROXIDE DISMUTASE
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Organism Common	:	SPINACH
	Organism Scientific	:	SPINACIA OLERACEA
	Organism Taxid	:	3562

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:46 , HIS A:48 , HIS A:63 , HIS A:120	BINDING SITE FOR RESIDUE CU A 155
2	AC2	SOFTWARE	HIS A:63 , HIS A:71 , HIS A:80 , ASP A:83	BINDING SITE FOR RESIDUE ZN A 156
3	AC3	SOFTWARE	HIS B:46 , HIS B:48 , HIS B:63 , HIS B:120	BINDING SITE FOR RESIDUE CU B 155
4	AC4	SOFTWARE	HIS B:63 , HIS B:71 , HIS B:80 , ASP B:83 , THR B:136	BINDING SITE FOR RESIDUE ZN B 156
5	AC5	SOFTWARE	HIS C:46 , HIS C:48 , HIS C:63 , HIS C:120	BINDING SITE FOR RESIDUE CU C 155
6	AC6	SOFTWARE	HIS C:63 , HIS C:71 , HIS C:80 , ASP C:83 , THR C:136	BINDING SITE FOR RESIDUE ZN C 156
7	AC7	SOFTWARE	HIS D:46 , HIS D:48 , HIS D:63 , HIS D:120	BINDING SITE FOR RESIDUE CU D 155
8	AC8	SOFTWARE	HIS D:63 , HIS D:71 , HIS D:80 , ASP D:83	BINDING SITE FOR RESIDUE ZN D 156

Asymmetric/Biological Unit

No.	Residues
1	A:57	-	A:146
2	B:57	-	B:146
3	C:57	-	C:146
4	D:57	-	D:146

(no "Cis Peptide Bond" information available for 1SRD)

(no "SAP(SNP)/Variant" information available for 1SRD)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_1	PS00087	Copper/Zinc superoxide dismutase signature 1.	SODCP_SPIOL	112-122	4	A:44-54 B:44-54 C:44-54 D:44-54
2	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	SODCP_SPIOL	206-217	4	A:138-149 B:138-149 C:138-149 D:138-149

(no "Exon" information available for 1SRD)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:154
 aligned with SODCP_SPIOL | P07505 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:154
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
          SODCP_SPIOL    69 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 222
               SCOP domains d1srda_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                 SCOP domains
               CATH domains 1srdA00 A:1-154  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeee.....eeeeeeee.....eeeeeee.....eeeeeee.......hhhhhhh....................eeeeeeee.....eeeeeee.............eeeee.........................eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1srd A   1 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with SODCP_SPIOL | P07505 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:154
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
          SODCP_SPIOL    69 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 222
               SCOP domains d1srdb_ B: Cu,Zn superoxide dismutase, SOD                                                                                                                 SCOP domains
               CATH domains 1srdB00 B:1-154  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeee.....eeeeeeee.....eeeeeee.....eeeeeee.........hhhh.....................eeeeeeee.....eeeeeee.............eeeee.........................eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1srd B   1 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with SODCP_SPIOL | P07505 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:154
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
          SODCP_SPIOL    69 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 222
               SCOP domains d1srdc_ C: Cu,Zn superoxide dismutase, SOD                                                                                                                 SCOP domains
               CATH domains 1srdC00 C:1-154  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeeee.....eeeeeeee.....eeeeeee.....eeeeeee..................................eeeeeeee.....eeeeeee.............eeeee.........................eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1srd C   1 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:154
 aligned with SODCP_SPIOL | P07505 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:154
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
          SODCP_SPIOL    69 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 222
               SCOP domains d1srdd_ D: Cu,Zn superoxide dismutase, SOD                                                                                                                 SCOP domains
               CATH domains 1srdD00 D:1-154  [code=2.60.40.200, no name defined]                                                                                                       CATH domains
           Pfam domains (1) Sod_Cu-1srdD01 D:1-149                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) Sod_Cu-1srdD02 D:1-149                                                                                                                               ----- Pfam domains (2)
           Pfam domains (3) Sod_Cu-1srdD03 D:1-149                                                                                                                               ----- Pfam domains (3)
           Pfam domains (4) Sod_Cu-1srdD04 D:1-149                                                                                                                               ----- Pfam domains (4)
         Sec.struct. author eeeeeeeeee.....eeeeeeee.....eeeeeee.....eeeeeee..................................eeeeeeee.....eeeeeee.............eeeee.........................eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1srd D   1 ATKKAVAVLKGTSNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTDGVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

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)

Spinach (Spinacia oleracea) [TaxId: 3562] (1)

1a	d1srda_	A:
1b	d1srdb_	B:
1c	d1srdc_	C:
1d	d1srdd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.200, no name defined] (125)

Spinach (Spinacia oleracea) (1)

1a	1srdA00	A:1-154
1b	1srdB00	B:1-154
1c	1srdC00	C:1-154
1d	1srdD00	D:1-154

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sod_Cu] (71)

Family: Sod_Cu (71)

Spinacia oleracea (Spinach) (1)

1a	Sod_Cu-1srdD01	D:1-149
1b	Sod_Cu-1srdD02	D:1-149
1c	Sod_Cu-1srdD03	D:1-149
1d	Sod_Cu-1srdD04	D:1-149

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (SODCP_SPIOL | P07505)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0071486	cellular response to high light intensity	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a high light intensity stimulus.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Asymmetric/Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

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