4BX6 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   TRANS-DIVALENT STREPTAVIDIN

Authors :   M. Fairhead, D. Krndija, E. D. Lowe, M. Howarth

Date :   08 Jul 13 (Deposition) - 25 Sep 13 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

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

Reference :   M. Fairhead, D. Krndija, E. D. Lowe, M. Howarth
Plug-And-Play Pairing Via Defined Divalent Streptavidins.
J. Mol. Biol. V. 426 199 2014
PubMed-ID: 24056174 | Reference-DOI: 10.1016/J.JMB.2013.09.016

Molecule 1 - STREPTAVIDIN
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	RIPL
	Expression System Vector	:	PET21
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 37-163
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895
	Other Details	:	DEAD VARIANT

Molecule 2 - STREPTAVIDIN
	Chains	:	B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	RIPL
	Expression System Vector	:	PET21
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 37-163
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:120 , TRP D:79	BINDING SITE FOR RESIDUE MPD D1135
2	AC2	SOFTWARE	SER B:45 , ALA B:86 , HOH B:2040 , TRP D:120	BINDING SITE FOR RESIDUE MPD B1135
3	AC3	SOFTWARE	TRP B:79 , THR B:90 , TRP B:92 , TRP B:108 , ASP B:128 , HOH B:2017	BINDING SITE FOR RESIDUE MPD B1136

(no "SS Bond" information available for 4BX6)

(no "Cis Peptide Bond" information available for 4BX6)

(no "SAP(SNP)/Variant" information available for 4BX6)

Asymmetric 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

Biological Unit 1 (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 4BX6)

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 A 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 d4bx6a_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- 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
                 4bx6 A  16 GITGTWYAQLGDTFIVTAGADGALTGTYEAAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    25        35        45        55        65        75        85        95       105       115       125

Chain B 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 d4bx6b_ B: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee....eeeeeee....hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4bx6 B  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    25        35        45        55        65        75        85        95       105       115       125

Chain C from PDB  Type:PROTEIN  Length:121
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:121
                                    47        57        67        77        87        97       107       117       127       137       147       157 
            SAV_STRAV    38 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains d4bx6c_ C: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeeeee....eeeeeee...hhhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bx6 C  14 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    23        33        43        53        63        73        83        93       103       113       123       133

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 d4bx6d_ D: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- 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
                 4bx6 D  16 GITGTWYAQLGDTFIVTAGADGALTGTYEAAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 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 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: automated matches (50)

Streptomyces avidinii [TaxId: 1895] (27)

1a	d4bx6a_	A:
1b	d4bx6b_	B:
1c	d4bx6c_	C:
1d	d4bx6d_	D:

(no "CATH Domain" information available for 4BX6)

(no "Pfam Domain" information available for 4BX6)

Asymmetric 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 Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bx6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4bx6
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4bx5	CIS-DIVALENT STREPTAVIDIN
4bx7	TRANS-DIVALENT STREPTAVIDIN BOUND TO BIOTIN-4- FLUORESCEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Pfam Domains (0, 0)

Gene Ontology (1, 1)

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