2JGS - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CIRCULAR PERMUTANT OF AVIDIN

Authors :   J. A. E. Maatta, V. P. Hytonen, T. T. Airenne, E. Niskanen, M. S. Johnson, M. S. Kulomaa, H. R. Nordlund

Date :   14 Feb 07 (Deposition) - 04 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Biotin-Binding Protein, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. E. Maatta, T. T. Airenne, H. R. Nordlund, J. Janis, T. A. Paldanius P. Vainiotalo, M. S. Johnson, M. S. Kulomaa, V. P. Hytonen
Rational Modification Of Ligand-Binding Preference Of Avidin By Circular Permutation And Mutagenesis.
Chembiochem V. 9 1124 2008
PubMed-ID: 18381715 | Reference-DOI: 10.1002/CBIC.200700671

Molecule 1 - CIRCULAR PERMUTANT OF AVIDIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		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	BTN	4	Ligand/Ion	BIOTIN

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:28 , SER A:31 , SER A:33 , THR A:35 , TRP A:55 , MET A:76 , SER A:108 , TYR A:125 , THR A:127 , VAL A:129 , TRP B:68	BINDING SITE FOR RESIDUE BTN A1001
2	AC2	SOFTWARE	TRP A:68 , TRP B:28 , SER B:31 , SER B:33 , THR B:35 , TRP B:55 , MET B:76 , SER B:108 , TYR B:125 , THR B:127 , VAL B:129	BINDING SITE FOR RESIDUE BTN B1001
3	AC3	SOFTWARE	TRP C:28 , SER C:31 , SER C:33 , THR C:35 , TRP C:55 , MET C:76 , SER C:108 , TYR C:125 , THR C:127 , VAL C:129 , THR C:130 , HOH C:2038 , TRP D:68	BINDING SITE FOR RESIDUE BTN C1001
4	AC4	SOFTWARE	TRP C:68 , ARG D:17 , TRP D:28 , PHE D:30 , SER D:31 , SER D:33 , THR D:35 , TRP D:55 , MET D:76 , SER D:108 , TYR D:125 , THR D:127 , THR D:130 , HOH D:2055	BINDING SITE FOR RESIDUE BTN D1001

Asymmetric/Biological Unit

No.	Residues
1	A:41	-	A:96
2	B:41	-	B:96
3	C:41	-	C:96
4	D:41	-	D:96

(no "Cis Peptide Bond" information available for 2JGS)

(no "SAP(SNP)/Variant" information available for 2JGS)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	4	A:66-80 B:66-80 C:66-80 D:66-80

Asymmetric/Biological Unit (3, 12)

	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	0	-	-
1.4	ENSGALT00000003855	4	ENSGALE00000024240	Z:8501440-8501650	211	AVID_CHICK	28-98	71	4	A:4-32 B:1-32 (gaps) C:4-32 D:4-32	29 60 29 29
1.5	ENSGALT00000003855	5	ENSGALE00000024243	Z:8502076-8502196	121	AVID_CHICK	98-138	41	4	A:32-72 (gaps) B:32-72 C:32-72 D:32-72	41 41 41 41
1.6a	ENSGALT00000003855	6a	ENSGALE00000024241	Z:8502284-8502409	126	AVID_CHICK	138-152	15	4	A:72-120 (gaps) B:72-120 (gaps) C:72-120 (gaps) D:72-120 (gaps)	49 49 49 49

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:109
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:112
                                                                                                      146                 147  152          
                                    79        89        99       109       119       129       139      |  -         -      |150 |       -  
           AVID_CHICK    70 ESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTR-------------------LRTQKE----------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeeeee......eeeeeeeeee.---.eeeeeeeeee....hhhhhhh.eeeeeeeee.....eeee.....eeee.......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------AVIDIN_1       ----------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:4-32        ---------------------------------------Exon 1.6a  PDB: A:72-120 (gaps)   ---------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.5  PDB: A:32-72 (gaps)            ------------------------------------------- Transcript 1 (2)
                 2jgs A   4 ESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFID---KEVLKTMWLLRSSVNDIGDDWKATRVGIMIFTRCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVT 130
                                    13        23        33        43|   |   53        63        73      ||98       108       118       128  
                                                                   44  48                              80|                                  
                                                                                                        96

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:144
                                                                                                                                      147                  148 152          
                                    48        58        68        78        88        98       108       118       128       138        |-         -       148   |     -    
           AVID_CHICK    39 GSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL--------------------RTQKE----------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..----------------------------..eeeeeeee........eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee.....eeee.....eeee.......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------AVIDIN_1       ------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4  PDB: B:1-32 (gaps) UniProt: 28-98 [INCOMPLETE]    ---------------------------------------Exon 1.6a  PDB: B:72-120 (gaps)    ---------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.5  PDB: B:32-72 UniProt: 98-138   -------------------------------------------- Transcript 1 (2)
                 2jgs B   1 GS----------------------------KESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGIMIFTRLCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVT 130
                             |       -         -         -|       12        22        32        42        52        62        72        96       106       116       126    
                             2                            3                                                                            81|                                  
                                                                                                                                        96

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:112
                                                                                                      146                 147  152          
                                    79        89        99       109       119       129       139      |  -         -      |150 |       -  
           AVID_CHICK    70 ESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTR-------------------LRTQKE----------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeee.....eeee.....eeee.......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------AVIDIN_1       ----------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: C:4-32        ---------------------------------------Exon 1.6a  PDB: C:72-120 (gaps)   ---------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.5  PDB: C:32-72 UniProt: 98-138   ------------------------------------------- Transcript 1 (2)
                 2jgs C   4 ESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGIMIFTRCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVT 130
                                    13        23        33        43        53        63        73      ||98       108       118       128  
                                                                                                       80|                                  
                                                                                                        96

Chain D from PDB  Type:PROTEIN  Length:113
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:113
                                                                                                       147                  148 152          
                                    79        89        99       109       119       129       139       | -         -       149  |      -   
           AVID_CHICK    70 ESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL--------------------RTQKE----------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Avidin-2jgsD01 D:4-80                                                        ------------------------------------ Pfam domains (1)
           Pfam domains (2) Avidin-2jgsD02 D:4-80                                                        ------------------------------------ Pfam domains (2)
           Pfam domains (3) Avidin-2jgsD03 D:4-80                                                        ------------------------------------ Pfam domains (3)
           Pfam domains (4) Avidin-2jgsD04 D:4-80                                                        ------------------------------------ Pfam domains (4)
         Sec.struct. author .eeeeeee.........eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee.....eeee.....eeee.......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------AVIDIN_1       ------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4  PDB: D:4-32        ---------------------------------------Exon 1.6a  PDB: D:72-120 (gaps)    ---------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.5  PDB: D:32-72 UniProt: 98-138   -------------------------------------------- Transcript 1 (2)
                 2jgs D   4 ESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGIMIFTRLCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVT 130
                                    13        23        33        43        53        63        73       |97       107       117       127   
                                                                                                        81|                                  
                                                                                                         96

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 '\|'

(no "SCOP Domain" information available for 2JGS)

(no "CATH Domain" information available for 2JGS)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Gallus gallus (Chicken) (13)

1a	Avidin-2jgsD01	D:4-80
1b	Avidin-2jgsD02	D:4-80
1c	Avidin-2jgsD03	D:4-80
1d	Avidin-2jgsD04	D:4-80

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (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/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
		BTN	[ 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 2jgs)

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
	2jgs
		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)

1avd	AVIDIN COMPLEX WITH BIOTIN
1ave	AVIDIN (APO FORM)
1ij8	CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX
1ldo	AVIDIN-NORBIOITN COMPLEX
1ldq	AVIDIN-HOMOBIOTIN COMPLEX
1lel	THE AVIDIN BCAP COMPLEX
1nqn	STRAYCTURE OF AVM-W110K (W110K MUTANT OF AVIDIN)
1rav	RECOMBINANT AVIDIN
1vyo	CRYSTAL STRUCTURE OF AVIDIN
2a5b	AVIDIN COMPLEXED WITH 8-OXODEOXYGUANOSINE
2a5c	STRUCTURE OF AVIDIN IN COMPLEX WITH THE LIGAND 8-OXODEOXYADENOSINE
2a8g	STRUCTURE OF AVIDIN IN COMPLEX WITH THE LIGANDDEOXYGUANOSINE
2avi	AVIDIN COMPLEX WITH BIOTIN
2c4i	CRYSTAL STRUCTURE OF ENGINEERED AVIDIN
2cam	AVIDIN MUTANT (K3E,K9E,R26D,R124L)

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 (3, 12)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

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