1SWG - JenaLib

Asym.Unit - manually (Jmol Viewer)

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)

Title :   CIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN

Authors :   S. Freitag, V. Chu, I. Le Trong, P. S. Stayton, R. E. Stenkamp

Date :   12 Jul 97 (Deposition) - 15 Jul 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   V. Chu, S. Freitag, I. Le Trong, R. E. Stenkamp, P. S. Stayton
Thermodynamic And Structural Consequences Of Flexible Loop Deletion By Circular Permutation In The Streptavidin-Biotin System.
Protein Sci. V. 7 848 1998
PubMed-ID: 9568892
(for further references see the PDB file header)

Molecule 1 - CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	T7
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	BTN	4	Ligand/Ion	BIOTIN

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	BTN	4	Ligand/Ion	BIOTIN

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	BTN	2	Ligand/Ion	BIOTIN

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	BTN	2	Ligand/Ion	BIOTIN

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:23 , LEU A:25 , SER A:27 , TYR A:43 , SER A:45 , TRP A:79 , ALA A:86 , SER A:88 , THR A:90 , TRP A:92 , TRP A:108 , ASP A:128 , TRP D:120	BINDING SITE FOR RESIDUE BTN A 600
2	AC2	SOFTWARE	ASN B:23 , LEU B:25 , SER B:27 , TYR B:43 , SER B:45 , TRP B:79 , ALA B:86 , SER B:88 , THR B:90 , TRP B:108 , LEU B:110 , ASP B:128 , HOH B:458 , TRP C:120 , ALA C:138 , SER C:139 , HOH C:453	BINDING SITE FOR RESIDUE BTN B 700
3	AC3	SOFTWARE	ASN C:23 , LEU C:25 , SER C:27 , TYR C:43 , SER C:45 , TRP C:79 , ALA C:86 , SER C:88 , THR C:90 , TRP C:92 , TRP C:108 , LEU C:110 , ASP C:128 , HOH C:521	BINDING SITE FOR RESIDUE BTN C 800
4	AC4	SOFTWARE	TRP A:120 , ASN D:23 , LEU D:25 , SER D:27 , TYR D:43 , SER D:45 , TRP D:79 , SER D:88 , THR D:90 , TRP D:92 , TRP D:108 , ASP D:128	BINDING SITE FOR RESIDUE BTN D 900

(no "SS Bond" information available for 1SWG)

Asymmetric Unit

No.	Residues
1	Lys C:134	-	Pro C:135

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	4	A:118-132 B:118-132 C:118-132 D:118-132

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	4	A:118-132 B:118-132 C:118-132 D:118-132

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	2	A:118-132 B:118-132 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	2	- - C:118-132 D:118-132

(no "Exon" information available for 1SWG)

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:112
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:112
                                                                                                             157                            
                                                                                                          156  |                       183  
                                    85        95       105       115       125       135       145       155|  |   163       173       183  
            SAV_STRAV    76 SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTK--VKPSAASIDAAKKAGVNNGNPLDAVQQ--   -
               SCOP domains d1swga_ A: Streptavidin                                                                                          SCOP domains
               CATH domains 1swgA00 A:52-46  [code=2.40.128.30, no name defined]                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee....eeee.....eeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------AVIDIN_1       ------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1swg A  52 SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKGITGTWYNQLGSTFIVTAGADGALTGTYESA  46
                                    61        71        81        91       101       111       121       131||      24        34        44  
                                                                                                          132|                              
                                                                                                            16

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:112
                                                                                                             157                            
                                                                                                          156  |                       183  
                                    85        95       105       115       125       135       145       155|  |   163       173       183  
            SAV_STRAV    76 SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTK--VKPSAASIDAAKKAGVNNGNPLDAVQQ--   -
               SCOP domains d1swgb_ B: Streptavidin                                                                                          SCOP domains
               CATH domains 1swgB00 B:52-46  [code=2.40.128.30, no name defined]                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee....eeee.....eeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------AVIDIN_1       ------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1swg B  52 SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKGITGTWYNQLGSTFIVTAGADGALTGTYESA  46
                                    61        71        81        91       101       111       121       131||      24        34        44  
                                                                                                          132|                              
                                                                                                            16

Chain C from PDB  Type:PROTEIN  Length:126
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:126
                                                                                                                           173              174      183  
                                    85        95       105       115       125       135       145       155       165       | -         -    |  179   |  
            SAV_STRAV    76 SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVN----------------NGNPLDAVQQ--   -
               SCOP domains d1swgc_ C: Streptavidin                                                                                                        SCOP domains
               CATH domains 1swgC00 C:52-46  [code=2.40.128.30, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..........eeeeeeee.........eeeeeeeeee.hhh.eeeeeeeeee...hhhhhh.eeeeeeeeeeee........hhhhhh.eeeee....eeeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------AVIDIN_1       --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1swg C  52 SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASGGGSAEAGITGTWYNQLGSTFIVTAGADGALTGTYESA  46
                                    61        71        81        91       101       111       121       131       141 ||     20        30        40      
                                                                                                                     143|                                 
                                                                                                                       13

Chain D from PDB  Type:PROTEIN  Length:113
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:113
                                                                                                            157 158                      183 
                                    84        94       104       114       124       134       144       154  |   |161       171       181 | 
            SAV_STRAV    75 ESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV---KPSAASIDAAKKAGVNNGNPLDAVQQ-   -
               SCOP domains d1swgd_ D: Streptavidin                                                                                           SCOP domains
               CATH domains 1swgD00 D:51-45  [code=2.40.128.30, no name defined]                                                              CATH domains
           Pfam domains (1) Avidin-1swgD01 D:51-132                                                           ------------------------------- Pfam domains (1)
           Pfam domains (2) Avidin-1swgD02 D:51-132                                                           ------------------------------- Pfam domains (2)
           Pfam domains (3) Avidin-1swgD03 D:51-132                                                           ------------------------------- Pfam domains (3)
           Pfam domains (4) Avidin-1swgD04 D:51-132                                                           ------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeeee....eeeee....eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------AVIDIN_1       ------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1swg D  51 ESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVGITGTWYNQLGSTFIVTAGADGALTGTYES  45
                                    60        70        80        90       100       110       120       130  ||    22        32        42   
                                                                                                            133|                             
                                                                                                              16

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: Streptavidin (121)

Streptomyces avidinii [TaxId: 1895] (121)

1a	d1swga_	A:
1b	d1swgb_	B:
1c	d1swgc_	C:
1d	d1swgd_	D:

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)

Streptomyces avidinii. Organism_taxid: 1895. (44)

1a	1swgD00	D:51-45
1b	1swgC00	C:52-46
1c	1swgA00	A:52-46
1d	1swgB00	B:52-46

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Streptomyces avidinii (97)

1a	Avidin-1swgD01	D:51-132
1b	Avidin-1swgD02	D:51-132
1c	Avidin-1swgD03	D:51-132
1d	Avidin-1swgD04	D:51-132

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SAV_STRAV | P22629)

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
		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
		Lys C:134 - Pro C:135	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 ](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
	1swg
		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
	SAV_STRAV \| P22629
		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
	SAV_STRAV \| P22629
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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 (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