Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-ORNITHYL-LYSINE
 
Authors :  T. G. Davies, J. R. H. Tame
Date :  11 Nov 98  (Deposition) - 16 Nov 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  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 Structure 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)

(-) Compounds

Molecule 1 - PERIPLASMIC OLIGOPEPTIDE-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-ORN-LYS
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ORN1Mod. Amino AcidL-ORNITHINE
3U18Ligand/IonURANIUM ATOM

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:245 , ASN A:247 , ASN A:366 , HIS A:371 , LYS B:3BINDING SITE FOR RESIDUE ACT A 518
2AC2SOFTWAREASP A:323 , ASN A:394 , HOH A:536 , HOH A:626BINDING SITE FOR RESIDUE U1 A 519
3AC3SOFTWAREHOH A:533 , HOH A:543 , HOH A:586 , HOH A:591BINDING SITE FOR RESIDUE U1 A 520
4AC4SOFTWAREHOH A:596 , HOH A:604 , HOH A:684BINDING SITE FOR RESIDUE U1 A 521
5AC5SOFTWAREGLU A:251 , ASP A:369 , HOH A:582 , HOH A:595 , HOH A:721BINDING SITE FOR RESIDUE U1 A 522
6AC6SOFTWAREGLU A:53 , ASP A:362 , ASP A:410 , HOH A:606BINDING SITE FOR RESIDUE U1 A 523
7AC7SOFTWAREASP A:133 , HIS A:517BINDING SITE FOR RESIDUE U1 A 524
8AC8SOFTWAREASP A:11 , HOH A:799BINDING SITE FOR RESIDUE U1 A 526

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:271 -A:417

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:282 -Pro A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B2H)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_5PS01040 Bacterial extracellular solute-binding proteins, family 5 signature.OPPA_SALTY87-108  1A:61-82

(-) Exons   (0, 0)

(no "Exon" information available for 1B2H)

(-) Sequences/Alignments

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 d1b2ha_ A: Oligo-peptide binding protein (OPPA)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1b2hA01 A:1-44,A:169-270,A:487-517          1b2hA02 A:45-168 Dipeptide-binding Protein; Domain 1                                                                        1b2hA01 A:1-44,A:169-270,A:487-517 Periplasmic binding protein-like II                                1b2hA03 A:271-486 Dipeptide-binding Protein; Domain 3                                                                                                                                                                   1b2hA01                         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
                 1b2h 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
                 1b2h B   1 KaK   3
                             | 
                             2-ORN
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B2H)

(-) Gene Ontology  (8, 8)

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).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    U1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:282 - Pro A:283   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1b2h
    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
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  OPPA_SALTY | P06202
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  OPPA_SALTY | P06202
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OPPA_SALTY | P06202: 1b05 1b0h 1b1h 1b32 1b3f 1b3g 1b3h 1b3l 1b40 1b46 1b4h 1b4z 1b51 1b52 1b58 1b5h 1b5i 1b5j 1b6h 1b7h 1b9j 1jet 1jeu 1jev 1ola 1olc 1qka 1qkb 1rkm 2olb 2rkm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B2H)