1RAV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   RECOMBINANT AVIDIN

Authors :   C. Rosano, P. Arosio, M. Bolognesi

Date :   27 Mar 98 (Deposition) - 15 Jul 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Avidin, Biotin Binding Protein, Calycins, Up-And-Down Beta Barrel, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Nardone, C. Rosano, P. Santambrogio, F. Curnis, A. Corti, F. Magni, A. G. Siccardi, G. Paganelli, R. Losso, B. Apreda, M. Bolognesi, A. Sidoli, P. Arosio
Biochemical Characterization And Crystal Structure Of A Recombinant Hen Avidin And Its Acidic Mutant Expressed In Escherichia Coli.
Eur. J. Biochem. V. 256 453 1998
PubMed-ID: 9760187 | Reference-DOI: 10.1046/J.1432-1327.1998.2560453.X
(for further references see the PDB file header)

Molecule 1 - AVIDIN
	Cell	:	EGG
	Cellular Location	:	CYTOPLASM (WHITE)
	Cell Line	:	BL21
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	BL21
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1RAV)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	B1	UNKNOWN	ASN A:12 , SER A:16 , TYR A:33 , THR A:35 , ASN A:118	NULL
2	B2	UNKNOWN	ASN B:12 , SER B:16 , TYR B:33 , THR B:35 , ASN B:118	NULL

Asymmetric Unit

No.	Residues
1	A:4	-	A:83
2	B:4	-	B:83

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AVID_CHICK_001 *	I	58	T	AVID_CHICK	---	---	A/B	I	34	T
	* ID not provided by source

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

Biological Unit 1 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AVID_CHICK_001 *	I	58	T	AVID_CHICK	---	---	A/B	I	34	T
	* ID not provided by source

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	AVID_CHICK	26-149	2	A:2-125 B:2-125
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	2	A:108-122 B:108-122

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	AVID_CHICK	26-149	4	A:2-125 B:2-125
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	4	A:108-122 B:108-122

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSGALT00000003855	1	ENSGALE00000024242	Z:8485802-8485882	81	AVID_CHICK	1-27	27	2	A:2-3 B:2-3	2 2
1.4	ENSGALT00000003855	4	ENSGALE00000024240	Z:8501440-8501650	211	AVID_CHICK	28-98	71	2	A:4-74 B:4-74	71 71
1.5	ENSGALT00000003855	5	ENSGALE00000024243	Z:8502076-8502196	121	AVID_CHICK	98-138	41	2	A:74-114 B:74-114	41 41
1.6a	ENSGALT00000003855	6a	ENSGALE00000024241	Z:8502284-8502409	126	AVID_CHICK	138-152	15	2	A:114-125 B:114-125	12 12

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:124
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:124
                                    35        45        55        65        75        85        95       105       115       125       135       145    
           AVID_CHICK    26 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRT 149
               SCOP domains d1rava_ A: Avidin                                                                                                            SCOP domains
               CATH domains 1ravA00 A:2-125  [code=2.40.128.30, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeee.......eeeeeeee.........eeeeeeeee..hhh....eeeeeee......eeeeeeeeee.....eeeeeeeeee.....hhhhhh.eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------T------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: A:2-125 UniProt: 26-149                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE (2)
           Transcript 1 (1) 1.Exon 1.4  PDB: A:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.5  PDB: A:74-114 UniProt: 98-138  ----------- Transcript 1 (2)
                 1rav A   2 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRT 125
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:124
                                    35        45        55        65        75        85        95       105       115       125       135       145    
           AVID_CHICK    26 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRT 149
               SCOP domains d1ravb_ B: Avidin                                                                                                            SCOP domains
               CATH domains 1ravB00 B:2-125  [code=2.40.128.30, no name defined]                                                                         CATH domains
           Pfam domains (1) --Avidin-1ravB01 B:4-122                                                                                                 --- Pfam domains (1)
           Pfam domains (2) --Avidin-1ravB02 B:4-122                                                                                                 --- Pfam domains (2)
         Sec.struct. author ......eeeee....eeee.......eeeeeeee.........eeeeeeeee..hhh....eeeeeee......eeeeeeeeee.....eeeeeeeeee.....hhhhhh.eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------T------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: B:2-125 UniProt: 26-149                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE (2)
           Transcript 1 (1) 1.Exon 1.4  PDB: B:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.5  PDB: B:74-114 UniProt: 98-138  ----------- Transcript 1 (2)
                 1rav B   2 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRT 125
                                    11        21        31        41        51        61        71        81        91       101       111       121

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: Streptavidin-like (225)

Superfamily: Avidin/streptavidin (197)

Family: Avidin/streptavidin (181)

Protein domain: Avidin (10)

Chicken (Gallus gallus) [TaxId: 9031] (10)

1a	d1rava_	A:
1b	d1ravb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.30, no name defined] (148)

Chicken (Gallus gallus) (26)

1a	1ravA00	A:2-125
1b	1ravB00	B:2-125

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Avidin] (113)

Family: Avidin (113)

Gallus gallus (Chicken) (13)

1a	Avidin-1ravB01	B:4-122
1b	Avidin-1ravB02	B:4-122

Asymmetric Unit(hide GO term definitions)

Chain A,B (AVID_CHICK | P02701)

cellular component
	GO:0005576		extracellular region		The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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
(no "Ligands, Modified Residues, Ions" information available for 1rav)

	Sites
		B1	[ RasMol ]	+environment [ RasMol ]
		B2	[ RasMol ]	+environment [ RasMol ]

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1rav
		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
	AVID_CHICK \| P02701
		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
	AVID_CHICK \| P02701
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (2, 4)

Exons (4, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (1, 1)

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