3PPP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURES OF THE SUBSTRATE-BINDING PROTEIN PROVIDE INSIGHTS INTO THE MULTIPLE COMPATIBLE SOLUTES BINDING SPECIFICITIES OF BACILLUS SUBTILIS ABC TRANSPORTER OPUC

Authors :   Y. Du, W. W. Shi, Y. X. He, Y. H. Yang, C. Z. Zhou, Y. Chen

Date :   25 Nov 10 (Deposition) - 11 May 11 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Alpha-Beta-Alpha Sandwich, Osmoprotectant, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Du, W. W. Shi, Y. X. He, Y. H. Yang, C. Z. Zhou, Y. Chen
Structures Of The Substrate-Binding Protein Provide Insight Into The Multiple Compatible Solute Binding Specificities O The Bacillus Subtilis Abc Transporter Opuc
Biochem. J. V. 436 283 2011
PubMed-ID: 21366542 | Reference-DOI: 10.1042/BJ20102097

Molecule 1 - GLYCINE BETAINE/CARNITINE/CHOLINE-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	OPUCC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	OPUCC, OSMOPROTECTANT-BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BET	2	Ligand/Ion	TRIMETHYL GLYCINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BET	1	Ligand/Ion	TRIMETHYL GLYCINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BET	1	Ligand/Ion	TRIMETHYL GLYCINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:39 , TYR A:91 , THR A:94 , ASN A:135 , TYR A:137 , TYR A:241 , HOH A:316 , HOH A:341	BINDING SITE FOR RESIDUE BET A 401
2	AC2	SOFTWARE	GLN B:39 , TYR B:91 , THR B:94 , ASN B:135 , TYR B:137 , TYR B:217 , TYR B:241 , HOH B:316	BINDING SITE FOR RESIDUE BET B 401

(no "SS Bond" information available for 3PPP)

(no "Cis Peptide Bond" information available for 3PPP)

(no "SAP(SNP)/Variant" information available for 3PPP)

(no "PROSITE Motif" information available for 3PPP)

(no "Exon" information available for 3PPP)

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:272
 aligned with OPUCC_BACSU | O32243 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:272
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  
          OPUCC_BACSU    32 DTIKIGAQSMTESEIVANMIAQLIEHDTDLNTALVKNLGSNYVQHQAMLGGDIDISATRYSGTDLTSTLGKEAEKDPKKALNIVQNEFQKRFSYKWFDSYGFDNTYAFTVTKKFAEKEHINTVSDLKKNASQYKLGVDNAWLKRKGDGYKGFVSTYGFEFGTTYPMQIGLVYDAVKNGKMDAVLAYSTDGRIKAYDLKILKDDKRFFPPYDCSPVIPEKVLKEHPELEGVINKLIGQIDTETMQELNYEVDGKLKEPSVVAKEFLEKHHYFD 303
               SCOP domains d3pppa_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhh....eeeeeehhhhhhh........hhhhhhhhhhhhhhhhhheee.........eeeeeehhhhhhhh..hhhhhhhhhhh.eeee..........hhhhhhhhhh....eeee.hhhhhhhhhhh....eeeee...hhhhhh.eee............eeeeeehhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ppp A  32 DTIKIGAQSMTESEIVANMIAQLIEHDTDLNTALVKNLGSNYVQHQAMLGGDIDISATRYSGTDLTSTLGKEAEKDPKKALNIVQNEFQKRFSYKWFDSYGFDNTYAFTVTKKFAEKEHINTVSDLKKNASQYKLGVDNAWLKRKGDGYKGFVSTYGFEFGTTYPMQIGLVYDAVKNGKMDAVLAYSTDGRIKAYDLKILKDDKRFFPPYDCSPVIPEKVLKEHPELEGVINKLIGQIDTETMQELNYEVDGKLKEPSVVAKEFLEKHHYFD 303
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

Chain B from PDB  Type:PROTEIN  Length:272
 aligned with OPUCC_BACSU | O32243 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:272
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  
          OPUCC_BACSU    32 DTIKIGAQSMTESEIVANMIAQLIEHDTDLNTALVKNLGSNYVQHQAMLGGDIDISATRYSGTDLTSTLGKEAEKDPKKALNIVQNEFQKRFSYKWFDSYGFDNTYAFTVTKKFAEKEHINTVSDLKKNASQYKLGVDNAWLKRKGDGYKGFVSTYGFEFGTTYPMQIGLVYDAVKNGKMDAVLAYSTDGRIKAYDLKILKDDKRFFPPYDCSPVIPEKVLKEHPELEGVINKLIGQIDTETMQELNYEVDGKLKEPSVVAKEFLEKHHYFD 303
               SCOP domains d3pppb_ B: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) OpuAC-3pppB01 B:32-298                                                                                                                                                                                                                                                     ----- Pfam domains (1)
           Pfam domains (2) OpuAC-3pppB02 B:32-298                                                                                                                                                                                                                                                     ----- Pfam domains (2)
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhh....eeeeeehhhhhhh........hhhhhhhhhhhhhhhhhheee.........eeeeeehhhhhhhh...hhhhh.hhhh.eeeeehhhhhh...hhhhhhhhhh....eeeeehhhhhhhhhhh....eeeee...hhhhhh.eee............eeeeeehhhhhhh.hhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ppp B  32 DTIKIGAQSMTESEIVANMIAQLIEHDTDLNTALVKNLGSNYVQHQAMLGGDIDISATRYSGTDLTSTLGKEAEKDPKKALNIVQNEFQKRFSYKWFDSYGFDNTYAFTVTKKFAEKEHINTVSDLKKNASQYKLGVDNAWLKRKGDGYKGFVSTYGFEFGTTYPMQIGLVYDAVKNGKMDAVLAYSTDGRIKAYDLKILKDDKRFFPPYDCSPVIPEKVLKEHPELEGVINKLIGQIDTETMQELNYEVDGKLKEPSVVAKEFLEKHHYFD 303
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

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: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: automated matches (267)

Protein domain: automated matches (267)

Bacillus subtilis [TaxId: 1423] (7)

1a	d3pppa_	A:
1b	d3pppb_	B:

(no "CATH Domain" information available for 3PPP)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: OpuAC (18)

Bacillus subtilis (6)

1a	OpuAC-3pppB01	B:32-298
1b	OpuAC-3pppB02	B:32-298

Asymmetric Unit(hide GO term definitions)

Chain A,B (OPUCC_BACSU | O32243)

molecular function
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006865	amino acid transport	The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071705	nitrogen compound transport	The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ppp)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
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Access by PDB/NDB ID
	3ppp
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	OPUCC_BACSU \| O32243
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	OPUCC_BACSU \| O32243
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UniProtKB/Swiss-Prot
	OPUCC_BACSU \| O32243	:	3ppn 3ppo 3ppq 3ppr

3ppn	THE SAME PROTEIN IN APO-FORM.
3ppo	THE SAME PROTEIN COMPLEXED WITH CARNITINE.
3ppq	THE SAME PROTEIN COMPLEXED WITH CHOLINE.
3ppr	THE SAME PROTEIN COMPLEXED WITH ECTOINE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (6, 6)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File