1DO5 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II

Authors :   A. L. Lamb, A. K. Wernimont, R. A. Pufahl, T. V. O'Halloran, A. C. Rosenzweig

Date :   18 Dec 99 (Deposition) - 18 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Beta-Barrel, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. L. Lamb, A. K. Wernimont, R. A. Pufahl, T. V. O'Halloran, A. C. Rosenzweig
Crystal Structure Of The Second Domain Of The Human Copper Chaperone For Superoxide Dismutase.
Biochemistry V. 39 1589 2000
PubMed-ID: 10677207 | Reference-DOI: 10.1021/BI992822I
(for further references see the PDB file header)

Molecule 1 - HUMAN COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE DOMAIN II
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24D
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS D:147 , HIS D:155 , HIS D:164 , ASP D:167	BINDING SITE FOR RESIDUE ZN D 27
2	AC2	SOFTWARE	HIS A:147 , HIS A:155 , HIS A:164 , ASP A:167	BINDING SITE FOR RESIDUE ZN A 28
3	AC3	SOFTWARE	HIS B:147 , HIS B:155 , HIS B:164 , ASP B:167	BINDING SITE FOR RESIDUE ZN B 29
4	AC4	SOFTWARE	HIS C:147 , HIS C:155 , HIS C:164 , ASP C:167	BINDING SITE FOR RESIDUE ZN C 30

Asymmetric Unit

No.	Residues
1	A:141	-	A:227
2	B:141	-	B:227
3	C:141	-	C:227
4	D:141	-	D:227

(no "Cis Peptide Bond" information available for 1DO5)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068078	R	163	W	CCS_HUMAN	Polymorphism	142340643	A/B/C/D	R	163	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068078	R	163	W	CCS_HUMAN	Polymorphism	142340643	A/B	R	163	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068078	R	163	W	CCS_HUMAN	Polymorphism	142340643	C/D	R	163	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068078	R	163	W	CCS_HUMAN	Polymorphism	142340643	A/B/C/D	R	163	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	CCS_HUMAN	219-230	4	A:219-230 B:219-230 C:219-230 D:219-230

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	CCS_HUMAN	219-230	2	A:219-230 B:219-230 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	CCS_HUMAN	219-230	2	- - C:219-230 D:219-230

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_CU_ZN_2	PS00332	Copper/Zinc superoxide dismutase signature 2.	CCS_HUMAN	219-230	4	A:219-230 B:219-230 C:219-230 D:219-230

(no "Exon" information available for 1DO5)

Asymmetric 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 CCS_HUMAN | O14618 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:154
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    
            CCS_HUMAN    84 QNLGAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSAGLF 237
               SCOP domains d1do5a_ A: Copper chaperone for superoxide dismutase, C-terminal domain                                                                                    SCOP domains
               CATH domains 1do5A00 A:84-237  [code=2.60.40.200, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......eeeeeeeeee..eeeeeeeee....eeeeeeee......hhhhh.......................eeeeeee....eeeeeeee...hhhhhh..eeeee......................eeeeee.eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------W-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------SOD_CU_ZN_2 ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1do5 A  84 QNLGAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSAGLF 237
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with CCS_HUMAN | O14618 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:148
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226        
            CCS_HUMAN    87 GAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSA 234
               SCOP domains d1do5b_ B: Copper chaperone for superoxide dismutase, C-terminal domain                                                                              SCOP domains
               CATH domains 1do5B00 B:87-234  [code=2.60.40.200, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......eeeeeeeeee..eeeeeeeee....eeeeeeee......hhhhh.......................eeeeeee.....eeeeeee...hhhhhh..eeeee......................eeeeee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------W----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1do5 B  87 GAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSA 234
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with CCS_HUMAN | O14618 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:148
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226        
            CCS_HUMAN    87 GAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSA 234
               SCOP domains d1do5c_ C: Copper chaperone for superoxide dismutase, C-terminal domain                                                                              SCOP domains
               CATH domains 1do5C00 C:87-234  [code=2.60.40.200, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeeeeee..eeeeeeeee....eeeeeeee......hhhhhhh.....................eeeeeee.....eeeeeee...hhhhhh..eeeee......................eeee...ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------W----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1do5 C  87 GAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSA 234
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226

Chain D from PDB  Type:PROTEIN  Length:153
 aligned with CCS_HUMAN | O14618 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:153
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234   
            CCS_HUMAN    85 NLGAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSAGLF 237
               SCOP domains d1do5d_ D: Copper chaperone for superoxide dismutase, C-terminal domain                                                                                   SCOP domains
               CATH domains 1do5D00 D:85-237  [code=2.60.40.200, no name defined]                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......eeeeeeeeee..eeeeeeeee....eeeeeeee...hhhhhhhhhh.....................eeeeeee.....eeeeeee...hhhhhh..eeeee......................eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------W-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------SOD_CU_ZN_2 ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1do5 D  85 NLGAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIARSAGLF 237
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234

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 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: Copper chaperone for superoxide dismutase, C-terminal domain (4)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1do5a_	A:
1b	d1do5b_	B:
1c	d1do5c_	C:
1d	d1do5d_	D:

Asymmetric 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)

Human (Homo sapiens) (52)

1a	1do5D00	D:85-237
1b	1do5B00	B:87-234
1c	1do5C00	C:87-234
1d	1do5A00	A:84-237

(no "Pfam Domain" information available for 1DO5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CCS_HUMAN | O14618)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
	GO:0016532	superoxide dismutase copper chaperone activity	A copper chaperone activity that specifically delivers copper to the Cu-Zn superoxide dismutase, to activate superoxide dismutase activity.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0015680	intracellular copper ion transport	The directed movement of copper (Cu) ions within a cell.
	GO:0030001	metal ion transport	The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0051353	positive regulation of oxidoreductase activity	Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the 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.
	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:0000302	response to reactive oxygen species	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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1qup	YEAST COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

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Exons (0, 0)

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