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

Asym./Biol. Unit (Jmol Viewer)

Title :   AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THE STREP-TAG II PEPTIDE: APO-SAM1

Authors :   I. P. Korndoerfer, A. Skerra

Date :   20 Nov 01 (Deposition) - 03 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Biotin, Crystal Structure, Protein Engineering, Strep-Tag, Streptavidin, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. P. Korndorfer, A. Skerra
Improved Affinity Of Engineered Streptavidin For The Strep-Tag Ii Peptide Is Due To A Fixed Open Conformation Of The Lid-Like Loop At The Binding Site.
Protein Sci. V. 11 883 2002
PubMed-ID: 11910031 | Reference-DOI: 10.1110/PS.4150102
(for further references see the PDB file header)

Molecule 1 - STREPTAVIDIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSA1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1KFF)

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

Asymmetric/Biological Unit

No.	Residues
1	Ala B:15	-	Gly B:16

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

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 1KFF)

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 d1kffa_ A: Streptavidin                                                                                                  SCOP domains
               CATH domains 1kffA00 A:16-135  [code=2.40.128.30, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....eeeeee....eeeeeee....hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kff A  16 GITGTWYNQLGSTFIVTAGADGALTGTYVTARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    25        35        45        55        65        75        85        95       105       115       125       135

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:120
                                    48        58        68        78        88        98       108       118       128       138       148       158
            SAV_STRAV    39 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains d1kffb_ B: Streptavidin                                                                                                  SCOP domains
               CATH domains 1kffB00 B:15-134  [code=2.40.128.30, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....eeeeee....eeeeeee....hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kff B  15 AGITGTWYNQLGSTFIVTAGADGALTGTYVTARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    24        34        44        54        64        74        84        94       104       114       124       134

Chain C from PDB  Type:PROTEIN  Length:119
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:119
                                    49        59        69        79        89        99       109       119       129       139       149         
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains d1kffc_ C: Streptavidin                                                                                                 SCOP domains
               CATH domains 1kffC00 C:16-134  [code=2.40.128.30, no name defined]                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee....eeeeeee....hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1kff C  16 GITGTWYNQLGSTFIVTAGADGALTGTYVTARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    25        35        45        55        65        75        85        95       105       115       125

Chain D from PDB  Type:PROTEIN  Length:119
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:119
                                    49        59        69        79        89        99       109       119       129       139       149         
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains d1kffd_ D: Streptavidin                                                                                                 SCOP domains
               CATH domains 1kffD00 D:16-134  [code=2.40.128.30, no name defined]                                                                   CATH domains
           Pfam domains (1) Avidin-1kffD01 D:16-132                                                                                              -- Pfam domains (1)
           Pfam domains (2) Avidin-1kffD02 D:16-132                                                                                              -- Pfam domains (2)
           Pfam domains (3) Avidin-1kffD03 D:16-132                                                                                              -- Pfam domains (3)
           Pfam domains (4) Avidin-1kffD04 D:16-132                                                                                              -- Pfam domains (4)
         Sec.struct. author ...eeee.....eeeeee....eeeeeee....hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1kff D  16 GITGTWYNQLGSTFIVTAGADGALTGTYVTARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    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	d1kffa_	A:
1b	d1kffb_	B:
1c	d1kffc_	C:
1d	d1kffd_	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	1kffC00	C:16-134
1b	1kffD00	D:16-134
1c	1kffA00	A:16-135
1d	1kffB00	B:15-134

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Streptomyces avidinii (97)

1a	Avidin-1kffD01	D:16-132
1b	Avidin-1kffD02	D:16-132
1c	Avidin-1kffD03	D:16-132
1d	Avidin-1kffD04	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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	Sites
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	Cis Peptide Bonds
		Ala B:15 - Gly B:16	[ RasMol ]

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1kl3	AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THE STREP-TAG II PEPTIDE : SAM1-STREPII
1kl4	AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THE STREP-TAG II PEPTIDE : APO-SAM2
1kl5	AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THE STREP-TAG II PEPTIDE : : SAM2-STREPII
1rsu	COMPLEX BETWEEN WILD-TYPE STREPTAVIDIN AND THE STREP-TAG II PEPTIDE

Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (1, 1)

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