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Title :   STRUCTURE-BASED DESIGN OF SYNTHETIC AZOBENZENE LIGANDS FOR STREPTAVIDIN

Authors :   P. C. Weber, F. R. Salemme

Date :   17 Feb 94 (Deposition) - 01 Nov 94 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   P. C. Weber, M. W. Pantoliano, D. M. Simons, F. R. Salemme
Structure-Based Design Of Synthetic Azobenzene Ligands For Streptavidin
J. Am. Chem. Soc. V. 116 2717 1994
PubMed: search
(for further references see the PDB file header)

Molecule 1 - STREPTAVIDIN
	Chains	:	A, B
	Engineered	:	YES
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAB	2	Ligand/Ion	2-((4'-HYDROXYNAPHTHYL)-AZO)BENZOIC ACID

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAB	4	Ligand/Ion	2-((4'-HYDROXYNAPHTHYL)-AZO)BENZOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:23 , SER A:27 , TYR A:43 , SER A:45 , VAL A:47 , GLY A:48 , ASN A:49 , ALA A:50 , TRP A:79 , ALA A:86 , SER A:88 , TRP A:108 , ASP A:128	BINDING SITE FOR RESIDUE NAB A 142
2	AC2	SOFTWARE	ASN B:23 , SER B:27 , TYR B:43 , SER B:45 , VAL B:47 , ASN B:49 , TRP B:79 , ARG B:84 , ALA B:86 , SER B:88 , TRP B:108 , ASP B:128	BINDING SITE FOR RESIDUE NAB B 142

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

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

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

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	1	A:13-133
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	2	A:118-132 B:118-132

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	2	A:13-133
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	4	A:118-132 B:118-132

(no "Exon" information available for 1SRJ)

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

    Alignment length:121
                                    46        56        66        76        86        96       106       116       126       136       146       156 
            SAV_STRAV    37 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1srja_ A: Streptavidin                                                                                                   SCOP domains
               CATH domains 1srjA00 A:13-133  [code=2.40.128.30, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhheeeee....eeeeee....eeeeeee.........eeeeeee.....---..eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee.....hhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: A:13-133 UniProt: 37-159                                                                                   PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1srj A  13 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPA---SGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    22        32        42        52        62  |   | 72        82        92       102       112       122       132 
                                                                               65  69

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:119
                                    48        58        68        78        88        98       108       118       128       138       148         
            SAV_STRAV    39 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1srjb_ B: Streptavidin                                                                                                 SCOP domains
               CATH domains 1srjB00 B:15-133  [code=2.40.128.30, no name define   d]                                                                CATH domains
           Pfam domains (1) Avidin-1srjB01 B:15-132                                                                                               - Pfam domains (1)
           Pfam domains (2) Avidin-1srjB02 B:15-132                                                                                               - Pfam domains (2)
         Sec.struct. author ....eeee.....eeeeee....eeeeeee........eeeeeeee.....---..eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: - UniProt: 37-159                                                                                        PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1srj B  15 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPA---SGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    24        34        44        54        64|   |   74        84        94       104       114       124         
                                                                             65  69

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	d1srja_	A:
1b	d1srjb_	B:

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 (38)

1a	1srjA00	A:13-133
1b	1srjB00	B:15-133

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Streptomyces avidinii (97)

1a	Avidin-1srjB01	B:15-132
1b	Avidin-1srjB02	B:15-132

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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Biological Unit
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