3IWX - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CISPLATIN BOUND TO A HUMAN COPPER CHAPERONE (DIMER)

Authors :   A. K. Boal, A. C. Rosenzweig

Date :   03 Sep 09 (Deposition) - 22 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

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

Keywords :   Beta-Alpha-Beta-Beta-Alpha-Beta, Transport Protein, Cisplatin, Platinum, Chaperone, Copper Transport, Ion Transport, Metal-Binding, Transport, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Boal, A. C. Rosenzweig
Crystal Structures Of Cisplatin Bound To A Human Copper Chaperone.
J. Am. Chem. Soc. V. 131 14196 2009
PubMed-ID: 19807176 | Reference-DOI: 10.1021/JA906363T

Molecule 1 - COPPER TRANSPORT PROTEIN ATOX1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ATOX1, HAH1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	METAL TRANSPORT PROTEIN ATX1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CPT	1	Ligand/Ion	CISPLATIN
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:11 , CYS A:12 , CYS A:15 , THR B:11 , CYS B:12 , CYS B:15	BINDING SITE FOR RESIDUE CPT A 69
2	AC2	SOFTWARE	HIS A:46 , SER A:47 , THR A:50	BINDING SITE FOR RESIDUE SO4 A 71
3	AC3	SOFTWARE	GLY B:28 , HOH B:96 , HOH B:114 , HOH B:126	BINDING SITE FOR RESIDUE SO4 B 70
4	AC4	SOFTWARE	HIS B:46 , SER B:47 , THR B:50 , HOH B:91 , HOH B:120	BINDING SITE FOR RESIDUE SO4 B 71

(no "SS Bond" information available for 3IWX)

(no "Cis Peptide Bond" information available for 3IWX)

(no "SAP(SNP)/Variant" information available for 3IWX)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMA_1	PS01047	Heavy-metal-associated domain.	ATOX1_HUMAN	7-35	2	A:7-35 B:7-35
2	HMA_2	PS50846	Heavy-metal-associated domain profile.	ATOX1_HUMAN	10-68	2	A:10-68 B:10-68

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2c	ENST00000313115	2c	ENSE00001532783	chr5:151138210-151138107	104	ATOX1_HUMAN	1-2	2	2	A:2-2 B:2-2	1 1
1.5b	ENST00000313115	5b	ENSE00001212343	chr5:151131340-151131265	76	ATOX1_HUMAN	3-28	26	2	A:3-28 B:3-28	26 26
1.6b	ENST00000313115	6b	ENSE00001212334	chr5:151126010-151125840	171	ATOX1_HUMAN	28-68	41	2	A:28-68 B:28-68	41 41
1.6e	ENST00000313115	6e	ENSE00001532778	chr5:151122520-151122384	137	ATOX1_HUMAN	-	0	0	-	-

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:67
 aligned with ATOX1_HUMAN | O00244 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:67
                                    11        21        31        41        51        61       
           ATOX1_HUMAN    2 PKHEFSVDMTCGGCAEAVSRVLNKLGGVKYDIDLPNKKVCIESEHSMDTLLATLKKTGKTVSYLGLE 68
               SCOP domains d3iwxa_ A: ATX1 metallochaperone protein (ATOX1)                    SCOP domains
               CATH domains 3iwxA00 A:2-68  [code=3.30.70.100, no name defined]                 CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhh.eeeeee....eeeeee..hhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----HMA_1  PDB: A:7-35           --------------------------------- PROSITE (1)
                PROSITE (2) --------HMA_2  PDB: A:10-68 UniProt: 10-68                          PROSITE (2)
           Transcript 1 (1) 1Exon 1.5b  PDB: A:3-28    ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.6b  PDB: A:28-68 UniProt: 28-68    Transcript 1 (2)
                  3iwx A  2 PKHEFSVDMTCGGCAEAVSRVLNKLGGVKYDIDLPNKKVCIESEHSMDTLLATLKKTGKTVSYLGLE 68
                                    11        21        31        41        51        61

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with ATOX1_HUMAN | O00244 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:67
                                    11        21        31        41        51        61       
           ATOX1_HUMAN    2 PKHEFSVDMTCGGCAEAVSRVLNKLGGVKYDIDLPNKKVCIESEHSMDTLLATLKKTGKTVSYLGLE 68
               SCOP domains d3iwxb_ B: ATX1 metallochaperone protein (ATOX1)                    SCOP domains
               CATH domains 3iwxB00 B:2-68  [code=3.30.70.100, no name defined]                 CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhh.eeeeee....eeeeee..hhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----HMA_1  PDB: B:7-35           --------------------------------- PROSITE (1)
                PROSITE (2) --------HMA_2  PDB: B:10-68 UniProt: 10-68                          PROSITE (2)
           Transcript 1 (1) 1Exon 1.5b  PDB: B:3-28    ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.6b  PDB: B:28-68 UniProt: 28-68    Transcript 1 (2)
                  3iwx B  2 PKHEFSVDMTCGGCAEAVSRVLNKLGGVKYDIDLPNKKVCIESEHSMDTLLATLKKTGKTVSYLGLE 68
                                    11        21        31        41        51        61

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: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: HMA, heavy metal-associated domain (79)

Family: HMA, heavy metal-associated domain (59)

Protein domain: ATX1 metallochaperone protein (ATOX1) (16)

Human (Homo sapiens), HAH1 [TaxId: 9606] (10)

1a	d3iwxa_	A:
1b	d3iwxb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.100, no name defined] (82)

Human (Homo sapiens) (29)

1a	3iwxA00	A:2-68
1b	3iwxB00	B:2-68

(no "Pfam Domain" information available for 3IWX)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ATOX1_HUMAN | O00244)

molecular function
	GO:0016531	copper chaperone activity	Assists in the delivery of copper ions to target proteins or compartments.
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0005375	copper ion transmembrane transporter activity	Catalysis of the transfer of copper (Cu) ions from one side of a membrane to the other.
	GO:0032767	copper-dependent 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), in the presence of copper.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016530	metallochaperone activity	Assists in the delivery of metal ions to target proteins or compartments.
	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).
biological process
	GO:0006878	cellular copper ion homeostasis	Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
	GO:0035434	copper ion transmembrane transport	The directed movement of copper cation across a membrane.
	GO:0006825	copper ion transport	The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015680	intracellular copper ion transport	The directed movement of copper (Cu) ions within a cell.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0006979	response to oxidative stress	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 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:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CPT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3iwx)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3iwx
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ATOX1_HUMAN \| O00244
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ATOX1_HUMAN \| O00244
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ATOX1_HUMAN \| O00244	:	1fe0 1fe4 1fee 1tl4 1tl5 2k1r 2lq9 3cjk 3iwl 4qot 4ydx 4yea 5f0w 5t7l

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (3, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File