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

(-) Description

Title :  CRYSTAL STRUCTURE OF A TRANSPORTER
 
Authors :  P. Zhang, K. Xu, M. Zhang, Q. Zhao, F. Yu
Date :  03 Nov 12  (Deposition) - 17 Apr 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,S,T
Keywords :  Transporter, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Xu, M. Zhang, Q. Zhao, F. Yu, H. Guo, C. Wang, F. He, J. Ding, P. Zhang
Crystal Structure Of A Folate Energy-Coupling Factor Transporter From Lactobacillus Brevis.
Nature V. 497 268 2013
PubMed-ID: 23584589  |  Reference-DOI: 10.1038/NATURE12046

(-) Compounds

Molecule 1 - ENERGY-COUPLING FACTOR TRANSPORTER ATP-BINDING PROTEIN ECFA 1
    Chains: A
    EC Number: 3.6.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET/PRSFDUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBIO1, ECFA1, LVIS_1661, UNKNOWN TRANSPORTER
    Organism Scientific: LACTOBACILLUS BREVIS
    Organism Taxid: 387344
    Strain: ATCC 367 / JCM 1170
    Synonym: ECF TRANSPORTER A COMPONENT ECFA 1
 
Molecule 2 - ENERGY-COUPLING FACTOR TRANSPORTER ATP-BINDING PROTEIN ECFA 2
    Chains: B
    EC Number: 3.6.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Gene: ECFA2, CBIO2, LVIS_1662
    Organism Scientific: LACTOBACILLUS BREVIS
    Organism Taxid: 387344
    Strain: ATCC 367 / JCM 1170
    Synonym: ECF TRANSPORTER A COMPONENT ECFA 2
 
Molecule 3 - UNCHARACTERIZED PROTEIN
    Chains: S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 4-177
    Gene: LVIS_0823
    Organism Scientific: LACTOBACILLUS BREVIS
    Organism Taxid: 387344
    Strain: ATCC 367 / JCM 1170
 
Molecule 4 - ENERGY-COUPLING FACTOR TRANSPORTER TRANSMEMBRANE PROTEIN ECFT
    Chains: T
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Gene: ECFT, LVIS_1660
    Organism Scientific: LACTOBACILLUS BREVIS
    Organism Taxid: 387344
    Strain: ATCC 367 / JCM 1170
    Synonym: ECF TRANSPORTER T COMPONENT ECFT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4HUQ)

(-) Sites  (0, 0)

(no "Site" information available for 4HUQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr B:15 -Asp B:16
2Gly S:54 -Pro S:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HUQ)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.......eeeeeee..ee....eeeee.....hhhhhhhhh.......eeeeee..eee....hhhhhhhhhhheeee..hhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhh.eeeeee..eeeeeehhhhhh.hhhhhhhh....hhhhhhhhhhhhh.........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4huq A   2 AIAFEHVTYTYQAGTPMAHTALTDVSLTVPDRGYLAIIGHTGSGKSTLIQQLNALLKPTSGTIKIDEFTITPETTNAALKPLRQHVGMVFQFPENQLFEETVRQDIAFGPKNFGMADADALALADEMLTTVGLDQSYAERSPFELSGGQMRRVAIAGVLAMQPKVLVLDEPTAGLDPQGRQEMMRLFARLHQEQGLTIVLVTHQMEDVAQYAEQVAVMHEGRLMKFGTPADVFSNREWLQDHQLDVPQAAQFARRLRDRGLTFPKQPLTADQLADYLAQQWAQR 285
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281    


Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...........eeeeeeee....eeeeee....hhhhhhhhh.......eeeeee..ee....hhhhhhh.eeee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhh..hhhhh.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4huq B   3 ENIISVDHLTYQYDENQAPALTDVSFTVHAGEWLAIVGHNGSGKSTLAKSLDGLLPFTQGSVTVGGITLTPETVWQVREQIGMIFQNPDNQFVGATVEDDVAFGLENRQISRDEMVPRVQAALAQVGMTSFAQREPSSLSGGQKQRVALAGIVAIAPKILILDEATSMLDPQGRIEMLAIVRQLRQQQNLTVISITHDIDEAASADRVLVIDDGRLVDEAVPSQIFERGTQLVEMGLDLPFTEKLKAALRQRGITPPTTYQTAAEMEEWLWQSLS 277
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     


Chain S from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..ee....ee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4huq S  10 DTLSMVTMGVLMALQLVISRFSVGNNFIKVSFTFLIVALIAKWFGPWWGMLTAAVVDVIGTLMTGGPFFIGFTVSAVLGSLIYAVFLYRQPVSWWRVIGASVLIALLVNTLLNTLWVTIMYQTPFWSLLPVRALKELIVTPVQIVLVYLLLKSQVIQMIQARLN 173
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169    


Chain T from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4huq T   6 FGRYLPLDSVVHRLDPRAKLMLSFCYIIVVFLANNIWSYAILIAFTVGAILSSKISLGFFLKGIRPLLWLIVFTVVLQLLFSINVTQDGLINAGYIFVRFLLIIMMSTLLTLSTQPLDIATGLASLMKPLRWVKVPVDTLAMMLSIALRFVPTLMDEATKIMNAQRARGVDFGEGGLFKQAKSLIPLMVPLFMSAFNRAEDLSTAMEARGYQDSEHRSQYRILTWQRRDTVTWLLFLLGFVAILI 262
                                    15        25        35        45        55        65        75        85 ||    107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257     
                                                                                                            87|                                                                                                                                                                  
                                                                                                            100
   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 4HUQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 25)

Asymmetric/Biological Unit(hide GO term definitions)

 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
(no "Ligands, Modified Residues, Ions" information available for 4huq)
 
  Sites
(no "Sites" information available for 4huq)
 
  Cis Peptide Bonds
    Gly S:54 - Pro S:55   [ RasMol ]  
    Tyr B:15 - Asp B:16   [ 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 ](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
  4huq
    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
  ECFA1_LACBA | Q03PY5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ECFA2_LACBA | Q03PY6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ECFT_LACBA | Q03PY7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q03S56_LACBA | Q03S56
    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)
  3.6.3.-
    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
  ECFA1_LACBA | Q03PY5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ECFA2_LACBA | Q03PY6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ECFT_LACBA | Q03PY7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q03S56_LACBA | Q03S56
    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
        ECFA1_LACBA | Q03PY5: 4hzu 4rfs
        ECFA2_LACBA | Q03PY6: 4hzu 4rfs
        ECFT_LACBA | Q03PY7: 4hzu 4rfs

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HUQ)