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 :  INWARD-FACING CONFORMATION OF ABC HEME IMPORTER BHUUV FROM BURKHOLDERIA CENOCEPACIA
 
Authors :  Y. Naoe, N. Nakamura, A. Doi, Y. Shiro, H. Sugimoto
Date :  25 Apr 16  (Deposition) - 16 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Metal-Binding, Membrane Protein, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Naoe, N. Nakamura, A. Doi, M. Sawabe, H. Nakamura, Y. Shiro, H. Sugimoto
Crystal Structure Of Bacterial Haem Importer Complex In The Inward-Facing Conformation
Nat Commun V. 7 13411 2016
PubMed-ID: 27830695  |  Reference-DOI: 10.1038/NCOMMS13411

(-) Compounds

Molecule 1 - PUTATIVE HEMIN ABC TRANSPORT SYSTEM, MEMBRANE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-19B
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HMUU, BCAM2629
    Organism Scientific: BURKHOLDERIA CENOCEPACIA J2315
    Organism Taxid: 216591
    Strain: J2315
    Synonym: HEME IMPORTER TRANSMEMBRANE SUBUNIT BHUU
 
Molecule 2 - HEMIN IMPORT ATP-BINDING PROTEIN HMUV
    Chains: C, D
    EC Number: 3.6.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-19B
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HMUV, BCAM2630
    Organism Scientific: BURKHOLDERIA CENOCEPACIA J2315
    Organism Taxid: 216591
    Strain: J2315
    Synonym: HEME IMPORTER ATP-BINDING SUBUNIT BHUV

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1DMU2Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:78 , ASP A:79 , LEU A:90 , TRP A:219 , ALA A:223 , ALA A:226binding site for residue DMU A 401
2AC2SOFTWAREVAL B:86 , ALA B:223binding site for residue DMU B 401
3AC3SOFTWAREARG C:35 , ASN C:36 , GLY C:37 , ALA C:38 , GLY C:39 , LYS C:40 , SER C:41binding site for residue SO4 C 301
4AC4SOFTWAREARG D:35 , ASN D:36 , GLY D:37 , ALA D:38 , GLY D:39 , LYS D:40 , SER D:41 , HOH D:403binding site for residue SO4 D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B57)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Arg A:168 -Gly A:169
2Ile A:285 -Gly A:286
3Ala A:331 -Pro A:332
4Val B:50 -Gly B:51
5Ser B:142 -Ala B:143
6Arg B:168 -Gly B:169
7Ile B:285 -Gly B:286
8Ala B:331 -Pro B:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B57)

(-) Exons   (0, 0)

(no "Exon" information available for 5B57)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b57 A  24 TSRRFAPFVLAALAILMGAMSVVALCVGAYRIPLAEAWAALSGDPAAQQARAVLLDIRAPRVVLALLVGGGFGATGAAMQALFRNPLADPGLVGVSSGAALGATTLIVLGPASAAALPVAAFAGGLAVAALVYRLAASRGRLALPLLLLAGIAINALVGAAIGLLTFVADDAQLRSLTFWSLGSLGGAQWPTLAAVAPCVALGGVLLVRERDALNALQLGETEALHLGVPVQRLKRRVLVAVALAVGALVSCAGIIGFIGLVAPHCVRLACGPDQRIVLPGAALLGALLTLAADLAARTVAAPADIPLGVLTALLGAPFFLALLWKNRGA 359
                                    33        43        53        63        73        83        93       103       113       123       133||     149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
                                                                                                                                        134|                                                                                                                                                                                                                          
                                                                                                                                         141                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b57 B  25 SRRFAPFVLAALAILMGAMSVVALCVGAYRIPLAEAWAALSGDPAAQQARAVLLDIRAPRVVLALLVGGGFGATGAAMQALFRNPLADPGLVGVSSGAALGATTLIVLGHASAAALPVAAFAGGLAVAALVYRLAASRGRLALPLLLLAGIAINALVGAAIGLLTFVADDAQLRSLTFWSLGSLGGAQWPTLAAVAPCVALGGVLLVRERDALNALQLGETEALHLGVPVQRLKRRVLVAVALAVGALVSCAGIIGFIGLVAPHCVRLACGPDQRIVLPGAALLGALLTLAADLAARTVAAPADIPLGVLTALLGAPFFLALLWKNRG 358
                                    34        44        54        64        74        84        94       104       114       124       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        
                                                                                                                                      133|                                                                                                                                                                                                                          
                                                                                                                                       140                                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeeeeeee....eeeee.....hhhhhhhhhhh..........eeeeeee..ee.hhhhhhhhhhheeee..........hhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhhhhhhh..eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b57 C   1 MLTAHHLDVAHGTILRDLSLSIEPGRVTALLGRNGAGKSTLLKTFAGELTGSVAGVRVTGDVTLNGEPLARIDAPRLACLRAVLPQAAQPAFPFSVDEIVLLGRYPHARRSGATSHRDRDIAWRALERAGADALVGRDVTTLSGGELARVQFARVLAQLWPDHPRYLLLDEPTAALDLAHQHRLLDTVRAVAREWQLGVLAIVHDPNLAARHADAIAMLADGTIVAHGAPRDVMTPAHIAQCYGFAVKMVETGPPVMVPA 273
                                    10|       22        32        42        52   ||   64        74        84        94       104       114       124       134       144       154       164  ||   180       190       200       210       220       230       240       250       260  ||   273
                                    10|                                         56|                                                                                                         167|                                                                                      263|      
                                     13                                          59                                                                                                          174                                                                                       267      


Chain D from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeeee....eeeeee....hhhhhhhhhhh.........eeeeeee..ee.hhhhhhhhh..eeee..........hhhhhhhhhh.....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhhhhhhh...eee.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b57 D   1 MLTAHHLDVAGTILRDLSLSIEPGRVTALLGRNGAGKSTLLKTFAGELTGSVGVRVTGDVTLNGEPLARIDAPRLACLRAVLPQAAQPAFPFSVDEIVLLGRYPHASHRDRDIAWRALERAGADALVGRDVTTLSGGELARVQFARVLAQLWPDHPRYLLLDEPTAALDLAHQHRLLDTVRAVAREWQLGVLAIVHDPNLAARHADAIAMLADGTIVAHGAPRDVMTPAHIAQCYGFAVKMVETGPPVMVPA 273
                                    10|       23        33        43        53 ||     66        76        86        96       106     ||122       132       142       152       162    || 178       188       198       208       218       228       238       248       258    || 271  
                                    10|                                       55|                                                  112|                                             167|                                                                                      263|      
                                     14                                        59                                                   119                                              174                                                                                       267
   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 5B57)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B57)

(-) Gene Ontology  (12, 15)

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
    DMU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 A:331 - Pro A:332   [ RasMol ]  
    Ala B:331 - Pro B:332   [ RasMol ]  
    Arg A:168 - Gly A:169   [ RasMol ]  
    Arg B:168 - Gly B:169   [ RasMol ]  
    Ile A:285 - Gly A:286   [ RasMol ]  
    Ile B:285 - Gly B:286   [ RasMol ]  
    Ser B:142 - Ala B:143   [ RasMol ]  
    Val B:50 - Gly B:51   [ 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
  5b57
    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
  B4EKB4_BURCJ | B4EKB4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  B4EKB5_BURCJ | B4EKB5
    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
  B4EKB4_BURCJ | B4EKB4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  B4EKB5_BURCJ | B4EKB5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B4EKB4_BURCJ | B4EKB4: 5b58
        B4EKB5_BURCJ | B4EKB5: 5b58

(-) Related Entries Specified in the PDB File

5b58