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Biological Unit 3 (Jmol Viewer)

Title :   STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 1.5, I222 COMPLEX

Authors :   B. A. Katz, R. T. Cass

Date :   03 Mar 97 (Deposition) - 18 Mar 98 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : B,D,M,P
Biol. Unit 1: B,D,M,P  (2x)
Biol. Unit 2: B,D,M,P  (4x)
Biol. Unit 3: B,D,M,P  (2x)

Keywords :   Complex (Biotin-Binding Protein-Peptide), Linear Thioether-Containing Peptide Engineered, Complex (Biotin-Binding Protein-Peptide) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Katz, R. T. Cass
In Crystals Of Complexes Of Streptavidin With Peptide Ligands Containing The Hpq Sequence The Pka Of The Peptide Histidine Is Less Than 3. 0.
J. Biol. Chem. V. 272 13220 1997
PubMed-ID: 9148939 | Reference-DOI: 10.1074/JBC.272.20.13220
(for further references see the PDB file header)

Molecule 1 - STREPTAVIDIN
	Chains	:	B, D
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895

Molecule 2 - PEPTIDE LIGAND CONTAINING HPQ
	Chains	:	M, P
	Engineered	:	YES

		1	2	3	4
Asymmetric Unit	:	B	D	M	P
Biological Unit 1 (2x)	:	B	D	M	P
Biological Unit 2 (4x)	:	B	D	M	P
Biological Unit 3 (2x)	:	B	D	M	P

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	LEA	2	Ligand/Ion	LEVULINIC ACID
2	NH2	2	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	LEA	4	Ligand/Ion	LEVULINIC ACID
2	NH2	4	Mod. Amino Acid	AMINO GROUP

Biological Unit 2 (2, 16)

No.	Name	Count	Type	Full Name
1	LEA	8	Ligand/Ion	LEVULINIC ACID
2	NH2	8	Mod. Amino Acid	AMINO GROUP

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	LEA	4	Ligand/Ion	LEVULINIC ACID
2	NH2	4	Mod. Amino Acid	AMINO GROUP

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS M:1 , HIS M:3 , PRO M:4 , HOH M:1028 , HOH M:1140	BINDING SITE FOR RESIDUE LEA M 2
2	AC2	SOFTWARE	CYS P:1 , HIS P:3 , PRO P:4	BINDING SITE FOR RESIDUE LEA P 2

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	2	B:13-135 D:13-133
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	2	B:118-132 D:118-132

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	4	B:13-135 D:13-133
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	4	B:118-132 D:118-132

Biological Unit 2 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	8	B:13-135 D:13-133
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	8	B:118-132 D:118-132

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	4	B:13-135 D:13-133
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	4	B:118-132 D:118-132

(no "Exon" information available for 1VWI)

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 B from PDB  Type:PROTEIN  Length:123
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:123
                                    46        56        66        76        86        96       106       116       126       136       146       156   
            SAV_STRAV    37 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d1vwib_ B: Streptavidin                                                                                                     SCOP domains
               CATH domains 1vwiB00 B:13-135  [code=2.40.128.30, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeee....eeeeee....eeeeeee........eeeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: B:13-135 UniProt: 37-159                                                                                     PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vwi B  13 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    22        32        42        52        62        72        82        92       102       112       122       132

Chain D from PDB  Type:PROTEIN  Length:121
 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 d1vwid_ D: Streptavidin                                                                                                   SCOP domains
               CATH domains 1vwiD00 D:13-133  [code=2.40.128.30, no name defined]                                                                     CATH domains
           Pfam domains (1) --Avidin-1vwiD01 D:15-132                                                                                               - Pfam domains (1)
           Pfam domains (2) --Avidin-1vwiD02 D:15-132                                                                                               - Pfam domains (2)
         Sec.struct. author .hhh..eeee.....eeeeee....eeeeeee........eeeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: D:13-133 UniProt: 37-159                                                                                   PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vwi D  13 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    22        32        42        52        62        72        82        92       102       112       122       132

Chain M from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1vwi M   3 HPQGPPCKx  10
                                 ||||
                                 8|||
                                  1||
                                   9|
                                   10-NH2

Chain P from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1vwi P   3 HPQGPPCKx  10
                                 ||||
                                 8|||
                                  1||
                                   9|
                                   10-NH2

Legend:		→ Mismatch	(orange background)
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	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	d1vwib_	B:
1b	d1vwid_	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. (29)

1a	1vwiD00	D:13-133
1b	1vwiB00	B:13-135

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Streptomyces avidinii (97)

1a	Avidin-1vwiD01	D:15-132
1b	Avidin-1vwiD02	D:15-132

Asymmetric Unit(hide GO term definitions)

Chain B,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
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