1XOC - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Title :   THE STRUCTURE OF THE OLIGOPEPTIDE-BINDING PROTEIN, APPA, FROM BACILLUS SUBTILIS IN COMPLEX WITH A NONAPEPTIDE.

Authors :   V. M. Levdikov, E. V. Blagova, J. A. Brannigan, L. Wright, A. A. Vagin, A. J. Wilkinson

Date :   06 Oct 04 (Deposition) - 25 Jan 05 (Release) - 10 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)
Biol. Unit 3: A,B  (2x)

Keywords :   Oligopeptide, Appa, Transport, Bacillus Subtilis, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. M. Levdikov, E. V. Blagova, J. A. Brannigan, L. Wright, A. A. Vagin, A. J. Wilkinson
The Structure Of The Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis In Complex With A Nonapeptide.
J. Mol. Biol. V. 345 879 2005
PubMed-ID: 15588833 | Reference-DOI: 10.1016/J.JMB.2004.10.089
(for further references see the PDB file header)

Molecule 1 - OLIGOPEPTIDE-BINDING PROTEIN APPA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMALP2
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	APPA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	OLIGOPEPTIDE ABC TRANSPORTER

Molecule 2 - NONAPEPTIDE VDSKNTSSW
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 15)

No.	Name	Count	Type	Full Name
1	ZN	15	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:162 , HOH A:602 , HOH A:615 , HOH A:699 , HOH A:773 , HOH A:901	BINDING SITE FOR RESIDUE ZN A 521
02	AC2	SOFTWARE	ASP A:205 , HOH A:564 , HOH A:706	BINDING SITE FOR RESIDUE ZN A 522
03	AC3	SOFTWARE	ASP A:77 , ASP A:304 , HIS A:492 , HOH A:604	BINDING SITE FOR RESIDUE ZN A 523
04	AC4	SOFTWARE	LYS A:371 , GLU A:374 , HOH A:654 , HOH A:815	BINDING SITE FOR RESIDUE ZN A 524
05	AC5	SOFTWARE	GLU A:130 , LYS A:140 , ZN A:535 , HOH A:796 , HOH A:845	BINDING SITE FOR RESIDUE ZN A 525
06	AC6	SOFTWARE	ASP A:171 , ZN A:528	BINDING SITE FOR RESIDUE ZN A 526
07	AC7	SOFTWARE	ASP A:83 , GLU A:136 , GLU A:306 , HOH A:658 , HOH A:686	BINDING SITE FOR RESIDUE ZN A 527
08	AC8	SOFTWARE	ASP A:171 , ASP A:375 , ZN A:526 , HOH A:765	BINDING SITE FOR RESIDUE ZN A 528
09	AC9	SOFTWARE	GLU A:449 , LYS A:476 , HOH A:953	BINDING SITE FOR RESIDUE ZN A 529
10	BC1	SOFTWARE	GLU A:118 , HOH A:659 , HOH A:809 , HOH A:829 , HOH A:853 , HOH A:919	BINDING SITE FOR RESIDUE ZN A 530
11	BC2	SOFTWARE	ASN A:348 , ASP A:350 , ILE A:352 , ASP A:354	BINDING SITE FOR RESIDUE ZN A 531
12	BC3	SOFTWARE	ASP A:134 , ASP A:324 , HOH A:954	BINDING SITE FOR RESIDUE ZN A 532
13	BC4	SOFTWARE	ASP A:43 , ASP A:47 , ASP A:509 , HOH A:610 , HOH A:950 , HOH A:951 , HOH A:952	BINDING SITE FOR RESIDUE ZN A 533
14	BC5	SOFTWARE	LYS A:113 , ASP A:114 , ASP A:224 , HOH A:681 , HOH A:948	BINDING SITE FOR RESIDUE ZN A 534
15	BC6	SOFTWARE	GLU A:130 , LYS A:140 , ASP A:261 , ZN A:525	BINDING SITE FOR RESIDUE ZN A 535

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

Asymmetric Unit

No.	Residues
1	Pro A:407	-	Pro A:408

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	APPA_BACSU	93-115	1	A:70-92

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	APPA_BACSU	93-115	1	A:70-92

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	APPA_BACSU	93-115	2	A:70-92

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	APPA_BACSU	93-115	2	A:70-92

(no "Exon" information available for 1XOC)

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:504
 aligned with APPA_BACSU | P42061 from UniProtKB/Swiss-Prot  Length:543

    Alignment length:504
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539    
           APPA_BACSU    40 KPQQGGDLVVGSIGEPTLFNSLYSTDDASTDIENMLYSFLTKTDEKLNVKLSLAESIKELDGGLAYDVKIKKGVKFHDGKELTADDVVFTYSVPLSKDYKGERGSTYEMLKSVEKKGDYEVLFKLKYKDGNFYNNALDSTAILPKHILGNVPIADLEENEFNRKKPIGSGPFKFKEWKQGQYIKLEANDDYFEGRPYLDTVTYKVIPDANAAVAQLQAGDINFFNVPATDYKTAEKFNNLKIVTDLALSYVYIGWNEKNELFKDKKVRQALTTALDRESIVSQVLDGDGEVAYIPESPLSWNYPKDIDVPKFEYNEKKAKQMLAEAGWKDTNGDGILDKDGKKFSFTLKTNQGNKVREDIAVVVQEQLKKIGIEVKTQIVEWSALVEQMNPPNWDFDAMVMGWSLSTFPDQYDIFHSSQIKKGLNYVWYKNAEADKLMKDAKSISDRKQYSKEYEQIYQKIAEDQPYTFLYYPNNHMAMPENLEGYKYHPKRDLYNIEKWWLAK 543
               SCOP domains d1xoca1 A:17-520 Oligo-peptide binding protein (OPPA)                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------------------SBP_bac_5-1xocA01 A:64-439                                                                                                                                                                                                                                                                                                                                                              --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.............hhhhhhhhhhhh...eee.....eee..eeeeeeehhh.eeeeee............hhhhhhhhhhhhhh......hhhhh..eeeeeeee..eeeeee....hhhhhhhhhhh...hhhhhh..hhhhh..hhhhh........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh.....ee.hhhhhhhhh....eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhh....ee.......................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhh.......eeeeeee......hhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.eeeeee.eeeeeee..ee...........hhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------SBP_BACTERIAL_5        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xoc A  17 KPQQGGDLVVGSIGEPTLFNSLYSTDDASTDIENMLYSFLTKTDEKLNVKLSLAESIKELDGGLAYDVKIKKGVKFHDGKELTADDVVFTYSVPLSKDYKGERGSTYEMLKSVEKKGDYEVLFKLKYKDGNFYNNALDSTAILPKHILGNVPIADLEENEFNRKKPIGSGPFKFKEWKQGQYIKLEANDDYFEGRPYLDTVTYKVIPDANAAEAQLQAGDINFFNVPATDYKTAEKFNNLKIVTDLALSYVYIGWNEKNELFKDKKVRQALTTALDRESIVSQVLDGDGEVAYIPESPLSWNYPKDIDVPKFEYNEKKAKQMLAEAGWKDTNGDGILDKDGKKFSFTLKTNQGNKVREDIAVVVQEQLKKIGIEVKTQIVEWSALVEQMNPPNWDFDAMVMGWSLSTFPDQYDIFHSSQIKKGLNYVWYKNAEADKLMKDAKSISDRKQYSKEYEQIYQKIAEDQPYTFLYYPNNHMAMPENLEGYKYHPKRDLYNIEKWWLAK 520
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516

Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...eee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1xoc B   1 VDSKNTSSW   9

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: Phosphate binding protein-like (463)

Protein domain: Oligo-peptide binding protein (OPPA) (34)

Bacillus subtilis [TaxId: 1423] (1)

d1xoca1

A:17-520

(no "CATH Domain" information available for 1XOC)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: SBP_bac_5 (33)

Bacillus subtilis (1)

SBP_bac_5-1xocA01

A:64-439

Asymmetric Unit(hide GO term definitions)

Chain A (APPA_BACSU | P42061)

molecular function
	GO:0015197	peptide transporter activity	Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
biological process
	GO:0030420	establishment of competence for transformation	The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation.
	GO:0015833	peptide transport	The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	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:0043190	ATP-binding cassette (ABC) transporter complex	A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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