1NZR - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE AZURIN MUTANT NICKEL-TRP48MET FROM PSEUDOMONAS AERUGINOSA AT 2.2 ANGSTROMS RESOLUTION

Authors :   L. -C. Tsai, L. Sjolin, V. Langer, N. Bonander, B. G. Karlsson, T. Vannga C. Hammann, H. Nar

Date :   09 Dec 94 (Deposition) - 27 Feb 95 (Release) - 16 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Electron Transport (Copper) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. C. Tsai, L. Sjolin, V. Langer, N. Bonander, B. G. Karlsson, T. Vanngard, C. Hammann, H. Nar
Structure Of The Azurin Mutant Nickel-Trp48Met From Pseudomonas Aeruginosa At 2. 2 A Resolution.
Acta Crystallogr. , Sect. D V. 51 711 1995
PubMed-ID: 15299800 | Reference-DOI: 10.1107/S0907444995001041
(for further references see the PDB file header)

Molecule 1 - AZURIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	NI	4	Ligand/Ion	NICKEL (II) ION
2	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	NO3	-1	Ligand/Ion	NITRATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:45 , HIS A:46 , CYS A:112 , HIS A:117 , MET A:121	BINDING SITE FOR RESIDUE NI A 129
2	AC2	SOFTWARE	GLY B:45 , HIS B:46 , CYS B:112 , PHE B:114 , HIS B:117 , MET B:121	BINDING SITE FOR RESIDUE NI B 129
3	AC3	SOFTWARE	GLY C:45 , HIS C:46 , CYS C:112 , HIS C:117 , MET C:121	BINDING SITE FOR RESIDUE NI C 129
4	AC4	SOFTWARE	GLY D:45 , HIS D:46 , CYS D:112 , HIS D:117 , MET D:121	BINDING SITE FOR RESIDUE NI D 129
5	AC5	SOFTWARE	CYS A:3 , CYS A:26 , LYS A:27 , GLN A:28 , PRO B:40 , ASN B:42 , LEU D:68	BINDING SITE FOR RESIDUE NO3 A 130

Asymmetric Unit

No.	Residues
1	A:3	-	A:26
2	B:3	-	B:26
3	C:3	-	C:26
4	D:3	-	D:26

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	4	A:105-121 B:105-121 C:105-121 D:105-121

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	2	A:105-121 - C:105-121 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	2	- B:105-121 - D:105-121

(no "Exon" information available for 1NZR)

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:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d1nzra_ A: Azurin                                                                                                                SCOP domains
               CATH domains 1nzrA00 A:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee......hhhh....eeee...hhhhhhhhhhh.........................eeeeeeehhh......eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzr A   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNMVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d1nzrb_ B: Azurin                                                                                                                SCOP domains
               CATH domains 1nzrB00 B:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee......hhhh....eeeehhhhhhhhhhhhhh.hhh.....................eeeeeeehhh......eeee.....hhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzr B   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNMVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d1nzrc_ C: Azurin                                                                                                                SCOP domains
               CATH domains 1nzrC00 C:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee......hhhh....eeeehhhhhhhhhhhhhh.hhh.....................eeeeeeehhh......eeee.....hhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzr C   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNMVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d1nzrd_ D: Azurin                                                                                                                SCOP domains
               CATH domains 1nzrD00 D:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
           Pfam domains (1) Copper-bind-1nzrD01 D:1-128                                                                                                      Pfam domains (1)
           Pfam domains (2) Copper-bind-1nzrD02 D:1-128                                                                                                      Pfam domains (2)
           Pfam domains (3) Copper-bind-1nzrD03 D:1-128                                                                                                      Pfam domains (3)
           Pfam domains (4) Copper-bind-1nzrD04 D:1-128                                                                                                      Pfam domains (4)
         Sec.struct. author ...eeeee..........eeeee....eeeeeee......hhhh....eeeehhhhhhhhhhhhhh.hhh.....................eeeeeeehhh......eeee.....hhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzr D   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNMVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

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: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: Azurin (95)

Pseudomonas aeruginosa [TaxId: 287] (78)

1a	d1nzra_	A:
1b	d1nzrb_	B:
1c	d1nzrc_	C:
1d	d1nzrd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Pseudomonas aeruginosa. Organism_taxid: 287 (10)

1a	1nzrA00	A:1-128
1b	1nzrB00	B:1-128
1c	1nzrC00	C:1-128
1d	1nzrD00	D:1-128

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Pseudomonas aeruginosa (25)

1a	Copper-bind-1nzrD01	D:1-128
1b	Copper-bind-1nzrD02	D:1-128
1c	Copper-bind-1nzrD03	D:1-128
1d	Copper-bind-1nzrD04	D:1-128

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (AZUR_PSEAE | P00282)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric 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
		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nzr)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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
	1nzr
		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
	AZUR_PSEAE \| P00282
		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
	AZUR_PSEAE \| P00282
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1NZR)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (7, 7)

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