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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-SAM2

Authors :   I. P. Korndoerfer, A. Skerra

Date :   11 Dec 01 (Deposition) - 03 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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 1KL4)

(no "Site" information available for 1KL4)

(no "SS Bond" information available for 1KL4)

(no "Cis Peptide Bond" information available for 1KL4)

(no "SAP(SNP)/Variant" information available for 1KL4)

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 1KL4)

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 d1kl4a_ A: Streptavidin                                                                                                  SCOP domains
               CATH domains 1kl4A00 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
                 1kl4 A  16 GITGTWYNQLGSTFIVTAGADGALTGTYIGARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 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 d1kl4b_ B: Streptavidin                                                                                                  SCOP domains
               CATH domains 1kl4B00 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
                 1kl4 B  15 AGITGTWYNQLGSTFIVTAGADGALTGTYIGARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 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 d1kl4c_ C: Streptavidin                                                                                                 SCOP domains
               CATH domains 1kl4C00 C:16-134  [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
                 1kl4 C  16 GITGTWYNQLGSTFIVTAGADGALTGTYIGARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 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 d1kl4d_ D: Streptavidin                                                                                                 SCOP domains
               CATH domains 1kl4D00 D:16-134  [code=2.40.128.30, no name defined]                                                                   CATH domains
           Pfam domains (1) Avidin-1kl4D01 D:16-132                                                                                              -- Pfam domains (1)
           Pfam domains (2) Avidin-1kl4D02 D:16-132                                                                                              -- Pfam domains (2)
           Pfam domains (3) Avidin-1kl4D03 D:16-132                                                                                              -- Pfam domains (3)
           Pfam domains (4) Avidin-1kl4D04 D:16-132                                                                                              -- Pfam domains (4)
         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
                 1kl4 D  16 GITGTWYNQLGSTFIVTAGADGALTGTYIGARGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 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	d1kl4a_	A:
1b	d1kl4b_	B:
1c	d1kl4c_	C:
1d	d1kl4d_	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	1kl4C00	C:16-134
1b	1kl4D00	D:16-134
1c	1kl4A00	A:16-135
1d	1kl4B00	B:15-134

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Streptomyces avidinii (97)

1a	Avidin-1kl4D01	D:16-132
1b	Avidin-1kl4D02	D:16-132
1c	Avidin-1kl4D03	D:16-132
1d	Avidin-1kl4D04	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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1kff	AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THE STREP-TAG II PEPTIDE : APO-SAM1
1kl3	AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THE STREP-TAG II PEPTIDE : SAM1-STREPII
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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