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Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF ELECTRON TRANSFER (COBALT-PROTEIN)

Authors :   N. Bonander, T. Vanngard, L. -C. Tsai, V. Langer, H. Nar, L. Sjolin

Date :   08 Oct 96 (Deposition) - 12 Mar 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   N. Bonander, T. Vanngard, L. C. Tsai, V. Langer, H. Nar, L. Sjolin
The Metal Site Of Pseudomonas Aeruginosa Azurin, Revealed By A Crystal Structure Determination Of The Co(Ii) Derivative And Co-Epr Spectroscopy.
Proteins V. 27 385 1997
PubMed-ID: 9094740 | Reference-DOI: 10.1002/(SICI)1097-0134(199703)27:3<385::AID-PROT6> 3.0.CO;2-C
(for further references see the PDB file header)

Molecule 1 - AZURIN
	Chains	:	A, B, C, D
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	COBALT FORM
	Synonym	:	COBALT-AXURIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CO	4	Ligand/Ion	COBALT (II) ION

Asymmetric Unit (4, 4)

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 CO 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 CO B 129
3	AC3	SOFTWARE	GLY C:45 , HIS C:46 , CYS C:112 , HIS C:117	BINDING SITE FOR RESIDUE CO C 129
4	AC4	SOFTWARE	GLY D:45 , HIS D:46 , CYS D:112 , PHE D:114 , HIS D:117 , MET D:121	BINDING SITE FOR RESIDUE CO D 129

Asymmetric/Biological 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 1VLX)

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

Asymmetric/Biological 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

(no "Exon" information available for 1VLX)

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: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 d1vlxa_ A: Azurin                                                                                                                SCOP domains
               CATH domains 1vlxA00 A:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee......hhhh....eeee...hhhhhhhhhhh.hhh.....................eeeeeeehhh......eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlx A   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 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 d1vlxb_ B: Azurin                                                                                                                SCOP domains
               CATH domains 1vlxB00 B:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeee.....eeeeeee......hhhh....eeeehhhhhhhhhhhhhh.hhh.....................eeeeeeehhh......eeee.....hhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlx B   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 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 d1vlxc_ C: Azurin                                                                                                                SCOP domains
               CATH domains 1vlxC00 C:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeee.....eeeeeee......hhhh....eeeehhhhhhhhhhhhhh.hhh.....................eeeeeeehhh......eeee.....hhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlx C   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 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 d1vlxd_ D: Azurin                                                                                                                SCOP domains
               CATH domains 1vlxD00 D:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
           Pfam domains (1) Copper-bind-1vlxD01 D:1-128                                                                                                      Pfam domains (1)
           Pfam domains (2) Copper-bind-1vlxD02 D:1-128                                                                                                      Pfam domains (2)
           Pfam domains (3) Copper-bind-1vlxD03 D:1-128                                                                                                      Pfam domains (3)
           Pfam domains (4) Copper-bind-1vlxD04 D:1-128                                                                                                      Pfam domains (4)
         Sec.struct. author ...eeeee..........eeee.....eeeeeee......hhhh....eeee...hhhhhhhhhhh.hhh.....................eeeeeeehhh......eeee.....hhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlx D   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 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/Biological 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	d1vlxa_	A:
1b	d1vlxb_	B:
1c	d1vlxc_	C:
1d	d1vlxd_	D:

Asymmetric/Biological 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	1vlxA00	A:1-128
1b	1vlxB00	B:1-128
1c	1vlxC00	C:1-128
1d	1vlxD00	D:1-128

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Pseudomonas aeruginosa (25)

1a	Copper-bind-1vlxD01	D:1-128
1b	Copper-bind-1vlxD02	D:1-128
1c	Copper-bind-1vlxD03	D:1-128
1d	Copper-bind-1vlxD04	D:1-128

Asymmetric/Biological 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/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (4, 4)

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