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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CORE-STREPTAVIDIN MUTANT W108F IN COMPLEX WITH BIOTIN AT PH 7.0

Authors :   S. Freitag, I. Le Trong, A. Chilkoti, L. A. Klumb, P. S. Stayton, R. E. Stenkamp

Date :   27 Jan 98 (Deposition) - 09 Feb 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Reference :   S. Freitag, I. Le Trong, A. Chilkoti, L. A. Klumb, P. S. Stayton, R. E. Stenkamp
Structural Studies Of Binding Site Tryptophan Mutants In The High-Affinity Streptavidin-Biotin Complex.
J. Mol. Biol. V. 279 211 1998
PubMed-ID: 9636711 | Reference-DOI: 10.1006/JMBI.1998.1735
(for further references see the PDB file header)

Molecule 1 - CORE-STREPTAVIDIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-210
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895
	Other Details	:	PET-210, NOVAGEN, INC., MADISON,WI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	BTN	3	Ligand/Ion	BIOTIN

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:23 , SER A:27 , TYR A:43 , SER A:45 , VAL A:47 , ASN A:49 , TRP A:79 , SER A:88 , THR A:90 , PHE A:108 , ASP A:128	BINDING SITE FOR RESIDUE BTN A 300
2	AC2	SOFTWARE	ASN C:23 , SER C:27 , TYR C:43 , SER C:45 , VAL C:47 , ASN C:49 , TRP C:79 , SER C:88 , ASP C:128 , HOH C:390	BINDING SITE FOR RESIDUE BTN C 500
3	AC3	SOFTWARE	ASN D:23 , SER D:27 , TYR D:43 , SER D:45 , VAL D:47 , ASN D:49 , TRP D:79 , SER D:88 , THR D:90 , ASP D:128	BINDING SITE FOR RESIDUE BTN D 600

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

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

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

Asymmetric/Biological 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

(no "Exon" information available for 1SWN)

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:120
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:120
                                    49        59        69        79        89        99       109       119       129       139       149       159
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d1swna_ A: Streptavidin                                                                                                  SCOP domains
               CATH domains 1swnA00 A:16-135  [code=2.40.128.30, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee......hhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1swn A  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQFLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    25        35        45        55        65        75        85        95       105       115       125       135

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1swnb_ B: Streptavidin                                                                                                SCOP domains
               CATH domains 1swnB00 B:16-133  [code=2.40.    128.30, no name defined]                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee----.hhh.eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1swn B  16 GITGTWYNQLGSTFIVTAGADGALTGTYE----NAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQFLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        |-   |    55        65        75        85        95       105       115       125        
                                                       44   49

Chain C from PDB  Type:PROTEIN  Length:118
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1swnc_ C: Streptavidin                                                                                                SCOP domains
               CATH domains 1swnC00 C:16-133  [code=2.40.128.30, no name defined]                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee......hhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1swn C  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQFLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        45        55        65        75        85        95       105       115       125

Chain D from PDB  Type:PROTEIN  Length:118
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1swnd_ D: Streptavidin                                                                                                SCOP domains
               CATH domains 1swnD00 D:16-133  [code=2.40.128.30, no name defined]                                                                  CATH domains
           Pfam domains (1) Avidin-1swnD01 D:16-132                                                                                              - Pfam domains (1)
           Pfam domains (2) Avidin-1swnD02 D:16-132                                                                                              - Pfam domains (2)
           Pfam domains (3) Avidin-1swnD03 D:16-132                                                                                              - Pfam domains (3)
           Pfam domains (4) Avidin-1swnD04 D:16-132                                                                                              - Pfam domains (4)
         Sec.struct. author ...eeee.....eeeeee....eeeeeee........eeeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee......hhh.eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1swn D  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQFLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        45        55        65        75        85        95       105       115       125

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: Streptavidin-like (225)

Superfamily: Avidin/streptavidin (197)

Family: Avidin/streptavidin (181)

Protein domain: Streptavidin (121)

Streptomyces avidinii [TaxId: 1895] (121)

1a	d1swna_	A:
1b	d1swnb_	B:
1c	d1swnc_	C:
1d	d1swnd_	D:

Asymmetric/Biological 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	1swnA00	A:16-135
1b	1swnC00	C:16-133
1c	1swnD00	D:16-133
1d	1swnB00	B:16-133

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Streptomyces avidinii (97)

1a	Avidin-1swnD01	D:16-132
1b	Avidin-1swnD02	D:16-132
1c	Avidin-1swnD03	D:16-132
1d	Avidin-1swnD04	D:16-132

Asymmetric/Biological 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/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 3)

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