Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1SDY

STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004784	molecular_function	superoxide dismutase activity
A	0005507	molecular_function	copper ion binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005758	cellular_component	mitochondrial intermembrane space
A	0005829	cellular_component	cytosol
A	0006801	biological_process	superoxide metabolic process
A	0006825	biological_process	copper ion transport
A	0006878	biological_process	intracellular copper ion homeostasis
A	0006882	biological_process	intracellular zinc ion homeostasis
A	0008270	molecular_function	zinc ion binding
A	0016209	molecular_function	antioxidant activity
A	0016491	molecular_function	oxidoreductase activity
A	0016670	molecular_function	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor
A	0019430	biological_process	removal of superoxide radicals
A	0031505	biological_process	fungal-type cell wall organization
A	0034599	biological_process	cellular response to oxidative stress
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0050821	biological_process	protein stabilization
A	1901856	biological_process	negative regulation of cellular respiration
A	1902693	cellular_component	superoxide dismutase complex
A	1990748	biological_process	cellular detoxification
B	0004784	molecular_function	superoxide dismutase activity
B	0005507	molecular_function	copper ion binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005758	cellular_component	mitochondrial intermembrane space
B	0005829	cellular_component	cytosol
B	0006801	biological_process	superoxide metabolic process
B	0006825	biological_process	copper ion transport
B	0006878	biological_process	intracellular copper ion homeostasis
B	0006882	biological_process	intracellular zinc ion homeostasis
B	0008270	molecular_function	zinc ion binding
B	0016209	molecular_function	antioxidant activity
B	0016491	molecular_function	oxidoreductase activity
B	0016670	molecular_function	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor
B	0019430	biological_process	removal of superoxide radicals
B	0031505	biological_process	fungal-type cell wall organization
B	0034599	biological_process	cellular response to oxidative stress
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046872	molecular_function	metal ion binding
B	0050821	biological_process	protein stabilization
B	1901856	biological_process	negative regulation of cellular respiration
B	1902693	cellular_component	superoxide dismutase complex
B	1990748	biological_process	cellular detoxification
C	0004784	molecular_function	superoxide dismutase activity
C	0005507	molecular_function	copper ion binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005758	cellular_component	mitochondrial intermembrane space
C	0005829	cellular_component	cytosol
C	0006801	biological_process	superoxide metabolic process
C	0006825	biological_process	copper ion transport
C	0006878	biological_process	intracellular copper ion homeostasis
C	0006882	biological_process	intracellular zinc ion homeostasis
C	0008270	molecular_function	zinc ion binding
C	0016209	molecular_function	antioxidant activity
C	0016491	molecular_function	oxidoreductase activity
C	0016670	molecular_function	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor
C	0019430	biological_process	removal of superoxide radicals
C	0031505	biological_process	fungal-type cell wall organization
C	0034599	biological_process	cellular response to oxidative stress
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
C	0046872	molecular_function	metal ion binding
C	0050821	biological_process	protein stabilization
C	1901856	biological_process	negative regulation of cellular respiration
C	1902693	cellular_component	superoxide dismutase complex
C	1990748	biological_process	cellular detoxification
D	0004784	molecular_function	superoxide dismutase activity
D	0005507	molecular_function	copper ion binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005758	cellular_component	mitochondrial intermembrane space
D	0005829	cellular_component	cytosol
D	0006801	biological_process	superoxide metabolic process
D	0006825	biological_process	copper ion transport
D	0006878	biological_process	intracellular copper ion homeostasis
D	0006882	biological_process	intracellular zinc ion homeostasis
D	0008270	molecular_function	zinc ion binding
D	0016209	molecular_function	antioxidant activity
D	0016491	molecular_function	oxidoreductase activity
D	0016670	molecular_function	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor
D	0019430	biological_process	removal of superoxide radicals
D	0031505	biological_process	fungal-type cell wall organization
D	0034599	biological_process	cellular response to oxidative stress
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
D	0046872	molecular_function	metal ion binding
D	0050821	biological_process	protein stabilization
D	1901856	biological_process	negative regulation of cellular respiration
D	1902693	cellular_component	superoxide dismutase complex
D	1990748	biological_process	cellular detoxification

Functional Information from PDB Data

site_id	A
Number of Residues	9
Details

Chain	Residue
A	HIS44
A	HIS46
A	HIS61
A	HIS118
A	HIS69
A	HIS78
A	ASP81
A	CU152
A	ZN153

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CU A 152

Chain	Residue
A	HIS44
A	HIS46
A	HIS61
A	HIS118
A	HOH154

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 153

Chain	Residue
A	HIS61
A	HIS69
A	HIS78
A	ASP81

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CU B 152

Chain	Residue
B	HIS44
B	HIS46
B	HIS61
B	HIS118
B	HOH154

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 153

Chain	Residue
B	HIS61
B	HIS69
B	HIS78
B	ASP81

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CU C 152

Chain	Residue
C	HIS44
C	HIS46
C	HIS61
C	HIS118
C	HOH154

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 153

Chain	Residue
C	HIS61
C	HIS69
C	HIS78
C	ASP81

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CU D 152

Chain	Residue
D	HIS44
D	HIS46
D	HIS61
D	HIS118
D	HOH154

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 153

Chain	Residue
D	HIS61
D	HIS69
D	HIS78
D	ASP81

site_id	B
Number of Residues	9
Details

Chain	Residue
B	HIS44
B	HIS46
B	HIS61
B	HIS118
B	HIS69
B	HIS78
B	ASP81
B	CU152
B	ZN153

site_id	C
Number of Residues	9
Details

Chain	Residue
C	HIS44
C	HIS46
C	HIS61
C	HIS118
C	HIS69
C	HIS78
C	ASP81
C	CU152
C	ZN153

site_id	D
Number of Residues	9
Details

Chain	Residue
D	HIS44
D	HIS46
D	HIS61
D	HIS118
D	HIS69
D	HIS78
D	ASP81
D	CU152
D	ZN153

Functional Information from PROSITE/UniProt

site_id	PS00087
Number of Residues	11
Details	SOD_CU_ZN_1 Copper/Zinc superoxide dismutase signature 1. GFHIHEfGDaT

Chain	Residue	Details
A	GLY42-THR52

site_id	PS00332
Number of Residues	12
Details	SOD_CU_ZN_2 Copper/Zinc superoxide dismutase signature 2. GNAGpRpACgvI

Chain	Residue	Details
A	GLY136-ILE147

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Binding site: {"description":"in apo form","evidences":[{"source":"PubMed","id":"10026301","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11524675","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10026301","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8652572","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10026301","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11524675","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"15665377","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	12
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)","evidences":[{"source":"PubMed","id":"15166219","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
A	HIS61
A	ARG141

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
B	HIS61
B	ARG141

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
C	HIS61
C	ARG141

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
D	HIS61
D	ARG141

site_id	CSA5
Number of Residues	1
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
A	HIS61

site_id	CSA6
Number of Residues	1
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
B	HIS61

site_id	CSA7
Number of Residues	1
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
C	HIS61

site_id	CSA8
Number of Residues	1
Details	Annotated By Reference To The Literature 2jcw

Chain	Residue	Details
D	HIS61

site_id	MCSA1
Number of Residues	8
Details	M-CSA 138

Chain	Residue	Details
A	HIS44	metal ligand
A	HIS46	metal ligand
A	HIS61	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
A	HIS69	metal ligand
A	HIS78	metal ligand
A	ASP81	metal ligand
A	HIS118	metal ligand
A	ARG141	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA2
Number of Residues	8
Details	M-CSA 138

Chain	Residue	Details
B	HIS44	metal ligand
B	HIS46	metal ligand
B	HIS61	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
B	HIS69	metal ligand
B	HIS78	metal ligand
B	ASP81	metal ligand
B	HIS118	metal ligand
B	ARG141	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA3
Number of Residues	8
Details	M-CSA 138

Chain	Residue	Details
C	HIS44	metal ligand
C	HIS46	metal ligand
C	HIS61	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
C	HIS69	metal ligand
C	HIS78	metal ligand
C	ASP81	metal ligand
C	HIS118	metal ligand
C	ARG141	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	8
Details	M-CSA 138

Chain	Residue	Details
D	HIS44	metal ligand
D	HIS46	metal ligand
D	HIS61	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
D	HIS69	metal ligand
D	HIS78	metal ligand
D	ASP81	metal ligand
D	HIS118	metal ligand
D	ARG141	electrostatic stabiliser, hydrogen bond donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)