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 :  STRUCTURE OF A TRI PEPTIDE BOUND POT FAMILY PEPTIDE TRANSPORTER
 
Authors :  J. A. Lyons, J. L. Parker, N. Solcan, A. Brinth, D. Li, S. T. A. Shah, M. Caf S. Newstead
Date :  09 May 14  (Deposition) - 25 Jun 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Major Facilitator Superfamily, Proton Oligopeptide Transporter (Pot) Family, Peptide Transporter, Tripeptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Lyons, J. L. Parker, N. Solcan, A. Brinth, D. Li, S. T. Shah, M. Caffrey, S. Newstead
Structural Basis For Polyspecificity In The Pot Family Of Proton-Coupled Oligopeptide Transporters.
Embo Rep. V. 15 886 2014
PubMed-ID: 24916388  |  Reference-DOI: 10.15252/EMBR.201338403

(-) Compounds

Molecule 1 - DI-OR TRIPEPTIDE:H+ SYMPORTER
    Atcc: BAA-250
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PWALDO-GFPD
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C43
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 264199
    Strain: LMG 18311
    Synonym: DI- OR TRIPEPTIDE PROTON SYMPORTER
 
Molecule 2 - ALANINE-TRIPEPTIDE
    Chains: B
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
178M3Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
278N3Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:85 , PRO A:86 , PHE A:89 , TYR A:193 , TYR A:194 , GLY A:197BINDING SITE FOR RESIDUE 78M A1479
2AC2SOFTWARELEU A:369 , ALA A:372 , ILE A:373 , ALA A:376 , VAL A:451 , 78N A:1481 , 78N A:1484BINDING SITE FOR RESIDUE 78N A1480
3AC3SOFTWARELEU A:212 , PRO A:214 , LEU A:221 , ALA A:376 , 78N A:1480 , 78N A:1484BINDING SITE FOR RESIDUE 78N A1481
4AC4SOFTWAREILE A:100 , ALA A:173 , VAL A:177 , SER A:180 , PHE A:187 , PHE A:195 , HOH A:2024BINDING SITE FOR RESIDUE 78M A1482
5AC5SOFTWARETYR A:335 , TYR A:378 , VAL A:384 , SER A:385 , LEU A:387 , TRP A:388 , 78N A:1484BINDING SITE FOR RESIDUE 78M A1483
6AC6SOFTWARELEU A:221 , SER A:225 , TYR A:378 , 78N A:1480 , 78N A:1481 , 78M A:1483BINDING SITE FOR RESIDUE 78N A1484
7AC7SOFTWAREASP A:48 , GLY A:107 , ALA A:108 , SER A:109BINDING SITE FOR RESIDUE PO4 A1485

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D2D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D2D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D2D)

(-) Exons   (0, 0)

(no "Exon" information available for 4D2D)

(-) 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:463
 aligned with Q5M4H8_STRT2 | Q5M4H8 from UniProtKB/TrEMBL  Length:483

    Alignment length:473
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475   
         Q5M4H8_STRT2     6 KTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMISSVKVTSTEHLRVVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKNQPSSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFLSKRIQGL 478
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.------hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d2d A   6 KTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMISS----STEHLRVVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKNQPSSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTK------NSQMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFLSKRIQGL 478
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265     |   -|      285       295       305       315       325       335       345       355       365       375       385       395       405       | -    |  425       435       445       455       465       475   
                                                                                                                                                                                                                                                                                                   271  276                                                                                                                                      413    420                                                          


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
                 4d2d B  31 AAA  33
   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  (0, 0)

(no "SCOP Domain" information available for 4D2D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D2D)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5M4H8_STRT2 | Q5M4H8)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    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:0006857    oligopeptide transport    The directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages.
    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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    78M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    78N  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4d2d)
 

(-) 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
  4d2d
    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
  Q5M4H8_STRT2 | Q5M4H8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q5M4H8_STRT2 | Q5M4H8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5M4H8_STRT2 | Q5M4H8: 4aps 4d2b 4d2c 4xni 4xnj 5d58 5d59 5d6k 5mmt

(-) Related Entries Specified in the PDB File

4d2b STRUCTURE OF A LIGAND FREE POT FAMILY PEPTIDE TRANSPORTER
4d2c STRUCTURE OF A DI PEPTIDE BOUND POT FAMILY PEPTIDE TRANSPORTER