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 :  CRYSTAL STRUCTURE OF MATE IN COMPLEX WITH MAD5
 
Authors :  Y. Tanaka, R. Ishitani, O. Nureki
Date :  27 Jul 12  (Deposition) - 03 Apr 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mate, Multidrug Transporter, Macrocyclic Peptide, Transport Protein, Transport Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tanaka, C. J. Hipolito, A. D. Maturana, K. Ito, T. Kuroda, T. Higuchi T. Katoh, H. E. Kato, M. Hattori, K. Kumazaki, T. Tsukazaki, R. Ishitani, H. Suga, O. Nureki
Structural Basis For The Drug Extrusion Mechanism By A Mate Multidrug Transporter.
Nature V. 496 247 2013
PubMed-ID: 23535598  |  Reference-DOI: 10.1038/NATURE12014

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF0708
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Strain: JCM 8422
    Synonym: ARCHAEAL-TYPE TRANSPORTER
 
Molecule 2 - MACROCYCLIC PEPTIDE
    Chains: B
    Engineered: YES
    Other Details: SELECTED BY THE RAPID SYSTEM PROTOCOL
    Synonym: MAD5
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2DPN1Mod. Amino AcidD-PHENYLALANINE
3OLC3Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:141 , TYR A:200BINDING SITE FOR RESIDUE OLC A 501
2AC2SOFTWAREHIS A:99 , ILE A:102 , ILE A:106 , THR A:190 , PHE A:232 , LEU A:239BINDING SITE FOR RESIDUE OLC A 502
3AC3SOFTWARELEU A:101 , SER A:210 , THR A:228 , LEU A:229BINDING SITE FOR RESIDUE OLC A 503
4AC4SOFTWAREGLN A:34 , TYR A:37 , ASN A:38 , PHE A:60 , MET A:64 , ILE A:67 , ALA A:71 , ASN A:153 , ASN A:154 , ALA A:172 , MET A:173 , ASN A:180 , THR A:209 , GLN A:253BINDING SITE FOR CHAIN B OF MACROCYCLIC PEPTIDE

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr B:3 -Ser B:4
2Val B:6 -Cys B:7
3Cys B:7 -Ala B:8
4Ala B:8 -Ala B:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VVR)

(-) 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:440
 aligned with Q8U2X0_PYRFU | Q8U2X0 from UniProtKB/TrEMBL  Length:461

    Alignment length:451
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453 
         Q8U2X0_PYRFU     4 KTTKGVQLLRGDPKKAIVRLSIPMMIGMSVQTLYNLADGIWVSGLGPESLAAVGLFFPVFMGIIALAAGLGVGTSSAIARRIGARDKEGADNVAVHSLILSLILGVTITITMLPAIDSLFRSMGAKGEAVELAIEYARVLLAGAFIIVFNNVGNGILRGEGDANRAMLAMVLGSGLNIVLDPIFIYTLGFGVVGAAYATLLSMVVTSLFIAYWLFVKRDTYVDITLRDFSPSREILKDILRVGLPSSLSQLSMSIAMFFLNSVAITAGGENGVAVFTSAWRITMLGIVPILGMAAATTSVTGAAYGERNVEKLETAYLYAIKIAFMIELAVVAFIMLFAPQVAYLFTYSESAQVIKGDLISALRTLPVFLVLTPFGMMTSAMFQGIGEGEKSLILTIFRTLVMQVGFAYIFVHYTTLGLRGVWIGIVIGNMVAAIVGFLWGRMRISALKKT 454
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.-.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vvr A   4 KTTKGVQLLRGDPKKAIVRLSIPMMIGMSVQTLYNLADGIWVSGLGPESLAAVGLFFPVFMGIIALAAGLGVGTSSAIARRIGARDKEGADNVAVHSLILSLILGVTITITMLPAIDSLFRSMGAKGEAVELAIEYARVLLAGAFIIVFNNVGNGILRGEGDANRAMLAMVLGSGLNIVLDPIFIYTLGFGVVGAAYATLLSMVVTSLFIAYWLFVKRDTYVDITLRDFSPSREILKDILRVGLPSSLSQLSMSIAMFFLNSVAITA-GENGVAVFTSAWRITMLGIVPILGMAAATTSVTGAAYGERNVEKLETAYLYAIKIAFMIELAVVAFIMLFAPQVAYLFTY------IKGDLISALRTLPVFLVLTPFGMMTSAMFQGIGEGEKSLILTIFRTLVMQVGFAYIFVH----GLRGVWIGIVIGNMVAAIVGFLWGRMRISALKKT 454
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      |273       283       293       303       313       323       333       343       | -    |  363       373       383       393       403       413  |    423       433       443       453 
                                                                                                                                                                                                                                                                                                    270 |                                                                            351    358                                                       416  421                                 
                                                                                                                                                                                                                                                                                                      272                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:12
                                            
               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
                 3vvr B   0 xxVYSAVCAAAA  11
                            ||       9  
                            0-ACE       
                             1-DPN
   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 3VVR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VVR)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8U2X0_PYRFU | Q8U2X0)
molecular function
    GO:0015297    antiporter activity    Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out).
    GO:0015238    drug transmembrane transporter activity    Enables the directed movement of a drug from one side of a membrane to the other. A drug is any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
biological process
    GO:0006855    drug transmembrane transport    The process in which a drug is transported from one side of a membrane to the other 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
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
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DPN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala B:8 - Ala B:9   [ RasMol ]  
    Cys B:7 - Ala B:8   [ RasMol ]  
    Tyr B:3 - Ser B:4   [ RasMol ]  
    Val B:6 - Cys B:7   [ 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
  3vvr
    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
  Q8U2X0_PYRFU | Q8U2X0
    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
  Q8U2X0_PYRFU | Q8U2X0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8U2X0_PYRFU | Q8U2X0: 3vvn 3vvo 3vvp 3vvs 3w4t 3wbn 4mlb

(-) Related Entries Specified in the PDB File

3vvn 3vvo 3vvp 3vvq 3vvs