1RKR - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AZURIN-I FROM ALCALIGENES XYLOSOXIDANS NCIMB 11015

Authors :   C. Li, T. Inoue, M. Gotowda, S. Suzuki, K. Yamaguchi, K. Kataoka, Y. Kai

Date :   17 May 97 (Deposition) - 20 May 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A  (2x)

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

Reference :   C. Li, T. Inoue, M. Gotowda, S. Suzuki, K. Yamaguchi, K. Kunishige, Y. Kai
Structure Of Azurin I From The Denitrifying Bacterium Alcaligenes Xylosoxidans Ncimb 11015 At 2. 45 A Resolution.
Acta Crystallogr. , Sect. D V. 54 347 1998
PubMed-ID: 9761902 | Reference-DOI: 10.1107/S0907444997010974
(for further references see the PDB file header)

Molecule 1 - AZURIN-I
	Chains	:	A, B, C, D
	Organism Scientific	:	ACHROMOBACTER XYLOSOXIDANS
	Organism Taxid	:	85698
	Strain	:	NCIMB 11015

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:45 , HIS A:46 , CYS A:112 , PHE A:114 , HIS A:117 , MET A:121	BINDING SITE FOR RESIDUE CU A 200
2	AC2	SOFTWARE	GLY B:45 , HIS B:46 , CYS B:112 , HIS B:117 , MET B:121	BINDING SITE FOR RESIDUE CU B 201
3	AC3	SOFTWARE	GLY C:45 , HIS C:46 , CYS C:112 , HIS C:117 , MET C:121	BINDING SITE FOR RESIDUE CU C 202
4	AC4	SOFTWARE	GLY D:45 , HIS D:46 , CYS D:112 , HIS D:117 , MET D:121	BINDING SITE FOR RESIDUE CU D 203

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 1RKR)

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

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.	AZUR1_ALCXX	105-121	4	A:105-121 B:105-121 C:105-121 D:105-121

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR1_ALCXX	105-121	1	A:105-121 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR1_ALCXX	105-121	1	- B:105-121 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR1_ALCXX	105-121	1	- - C:105-121 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR1_ALCXX	105-121	1	- - - D:105-121

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR1_ALCXX	105-121	2	A:105-121 - - -

(no "Exon" information available for 1RKR)

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:129
 aligned with AZUR1_ALCXX | P56547 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
          AZUR1_ALCXX     1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
               SCOP domains d1rkra_ A: Azurin                                                                                                                 SCOP domains
               CATH domains 1rkrA00 A:1-129 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
                 1rkr A   1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with AZUR1_ALCXX | P56547 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
          AZUR1_ALCXX     1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
               SCOP domains d1rkrb_ B: Azurin                                                                                                                 SCOP domains
               CATH domains 1rkrB00 B:1-129 Cupredoxins -  blue copper proteins                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee......hhhh....eeeehhhhhhhhhhhh...hhh.....................eeeeeeehhh......eeee.....hhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkr B   1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with AZUR1_ALCXX | P56547 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
          AZUR1_ALCXX     1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
               SCOP domains d1rkrc_ C: Azurin                                                                                                                 SCOP domains
               CATH domains 1rkrC00 C:1-129 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
                 1rkr C   1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with AZUR1_ALCXX | P56547 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
          AZUR1_ALCXX     1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
               SCOP domains d1rkrd_ D: Azurin                                                                                                                 SCOP domains
               CATH domains 1rkrD00 D:1-129 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
                 1rkr D   1 AECSVDIAGNDGMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMGHNWVLTKQADMQGAVNDGMAAGLDNNYVKKDDARVIAHTKVIGGGETDSVTFDVSKLAAGEDYAYFCSFPGHFALMKGVLKLVD 129
                                    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)

Alcaligenes xylosoxidans, NCIMB (11015), different isoforms [TaxId: 85698] (4)

1a	d1rkra_	A:
1b	d1rkrb_	B:
1c	d1rkrc_	C:
1d	d1rkrd_	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)

Achromobacter xylosoxidans. Organism_taxid: 85698. Strain: ncimb 11015 (1)

1a	1rkrA00	A:1-129
1b	1rkrB00	B:1-129
1c	1rkrC00	C:1-129
1d	1rkrD00	D:1-129

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (AZUR1_ALCXX | P56547)

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.
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
		CU	[ 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 1rkr)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]
		Biological Unit 5	[ 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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format \| Biol. Unit 5 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
	1rkr
		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
	AZUR1_ALCXX \| P56547
		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
	AZUR1_ALCXX \| P56547
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1RKR)

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

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 (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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