1B6H - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE

Authors :   T. G. Davies, J. R. H. Tame

Date :   13 Nov 98 (Deposition) - 18 Nov 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

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

Reference :   T. G. Davies, R. E. Hubbard, J. R. Tame
Relating Structure To Thermodynamics: The Crystal Structures And Binding Affinity Of Eight Oppa-Peptide Complexes.
Protein Sci. V. 8 1432 1999
PubMed-ID: 10422831
(for further references see the PDB file header)

Molecule 1 - PERIPLASMIC OLIGO-PEPTIDE BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Synonym	:	OPPA

Molecule 2 - LYS-NVA-LYS PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 9)

No.	Name	Count	Type	Full Name
1	NVA	1	Mod. Amino Acid	NORVALINE
2	U1	8	Ligand/Ion	URANIUM ATOM

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:323 , ASN A:394 , HOH A:535 , HOH A:677	BINDING SITE FOR RESIDUE U1 A 518
2	AC2	SOFTWARE	HOH A:527 , HOH A:556 , HOH A:614 , HOH A:639	BINDING SITE FOR RESIDUE U1 A 519
3	AC3	SOFTWARE	HOH A:578 , HOH A:701 , HOH A:722	BINDING SITE FOR RESIDUE U1 A 520
4	AC4	SOFTWARE	GLU A:251 , ASP A:369 , HOH A:735 , HOH A:807 , HOH A:813	BINDING SITE FOR RESIDUE U1 A 521
5	AC5	SOFTWARE	GLU A:53 , ASP A:362 , ASP A:410 , HOH A:676	BINDING SITE FOR RESIDUE U1 A 522
6	AC6	SOFTWARE	ASP A:133 , HIS A:517 , HOH A:530 , HOH A:580 , HOH A:590	BINDING SITE FOR RESIDUE U1 A 523
7	AC7	SOFTWARE	HOH A:1011	BINDING SITE FOR RESIDUE U1 A 524
8	AC8	SOFTWARE	ASP A:11 , GLU A:342 , HOH A:526 , HOH A:1050	BINDING SITE FOR RESIDUE U1 A 525

Asymmetric/Biological Unit

No.	Residues
1	A:271	-	A:417

Asymmetric/Biological Unit

No.	Residues
1	Ala A:282	-	Pro A:283

(no "SAP(SNP)/Variant" information available for 1B6H)

Asymmetric/Biological 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.	OPPA_SALTY	87-108	1	A:61-82

(no "Exon" information available for 1B6H)

Asymmetric/Biological 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:517
 aligned with OPPA_SALTY | P06202 from UniProtKB/Swiss-Prot  Length:543

    Alignment length:517
                                    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       526       536       
           OPPA_SALTY    27 ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 543
               SCOP domains d1b6ha_ A: Oligo-peptide binding protein (OPPA)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1b6hA01 A:1-44,A:169-270,A:487-517          1b6hA02 A:45-168 Dipeptide-binding Protein; Domain 1                                                                        1b6hA01 A:1-44,A:169-270,A:487-517 Periplasmic binding protein-like II                                1b6hA03 A:271-486 Dipeptide-binding Protein; Domain 3                                                                                                                                                                   1b6hA01                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee...............hhhhhhhhhh....eee.....eee..eeeeeee...eeeeee.............hhhhhhhhhhhh.hhh....hhhhhh.....hhhhh.....hhh..eeeee..eeeee.......hhhhhh.hhh....hhhhhhhhhh............eeeeeee...eeeeee......hhh....eeeee....hhhhhhhhh...............hhhhhhh.hhheeeee..eeeeeee.........hhhhhhhhhh..hhhhhh..........................hhhh..hhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh....eeeeeee.....hhhhhhhh.............hhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeee.eeeee..................hhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------SBP_BACTERIAL_5       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b6h A   1 ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH 517
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510

Chain B from PDB  Type:PROTEIN  Length:3
                                   
               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
                 1b6h B   1 KvK   3
                             | 
                             2-NVA

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/Biological Unit

Classes(

)

Folds(

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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)

Salmonella typhimurium [TaxId: 90371] (32)

d1b6ha_

(no "Pfam Domain" information available for 1B6H)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (OPPA_SALTY | P06202)

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: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: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: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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:282 - Pro A:283	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (8, 8)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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