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 COPROHEME BOUND HEMQ FROM LISTERIA MONOCYTOGENES
 
Authors :  D. Puehringer, G. Mlynek, S. Hofbauer, K. Djinovic-Carugo, C. Obinger
Date :  09 Aug 16  (Deposition) - 26 Oct 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Hemq, Heme Biosynthesis, Coproheme, Heme B, Gram-Positive Pathogens, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hofbauer, G. Mlynek, L. Milazzo, D. Puhringer, D. Maresch, I. Schaffner, P. G. Furtmuller, G. Smulevich, K. Djinovic-Carugo, C. Obinger
Hydrogen Peroxide-Mediated Conversion Of Coproheme To Heme By Hemq-Lessons From The First Crystal Structure And Kineti Studies.
Febs J. V. 283 4386 2016
PubMed-ID: 27758026  |  Reference-DOI: 10.1111/FEBS.13930

(-) Compounds

Molecule 1 - PUTATIVE HEME-DEPENDENT PEROXIDASE LMO2113
    Chains: A, B, C, D, E
    EC Number: 1.11.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21(+)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LMO2113
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Synonym: UPF0447 PROTEIN LMO2113, HEMQ

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1FEC5Ligand/Ion1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONICACID FERROUS COMPLEX
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NA5Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:63 , LEU A:64 , GLY A:65 , ALA A:68 , ASP A:69 , HOH A:401 , GLU B:86binding site for residue NA A 301
02AC2SOFTWARELEU A:110 , SER A:111 , TYR A:113 , ARG A:133 , TYR A:147 , MET A:149 , LYS A:151 , TRP A:159 , HIS A:174 , GLY A:178 , ARG A:179 , VAL A:185 , GLN A:186 , GLN A:187 , TRP A:200 , ILE A:215 , MET A:219 , SER A:225 , PHE A:231 , HOH A:425 , HOH A:442 , HOH A:477binding site for residue FEC A 302
03AC3SOFTWAREASN A:83 , ASN A:87 , SER C:62 , GLN C:244 , LYS C:247 , LEU C:248binding site for residue MPD A 303
04AC4SOFTWAREILE B:63 , LEU B:64 , GLY B:65 , ALA B:68 , HOH B:410 , GLU E:86binding site for residue NA B 301
05AC5SOFTWAREGLU B:109 , LEU B:110 , SER B:111 , ARG B:133 , TYR B:147 , MET B:149 , TRP B:159 , HIS B:174 , GLY B:178 , TYR B:181 , ALA B:182 , VAL B:185 , GLN B:187 , TRP B:200 , VAL B:202 , LEU B:204 , ILE B:215 , MET B:219 , SER B:225 , PHE B:231 , HOH B:403binding site for residue FEC B 302
06AC6SOFTWARELEU A:248 , GLU B:80 , ASN B:83 , ASN B:87 , HOH B:401binding site for residue MPD B 303
07AC7SOFTWAREGLU A:86 , ILE C:63 , LEU C:64 , GLY C:65 , ALA C:68 , HOH C:406binding site for residue NA C 301
08AC8SOFTWARESER C:111 , ASN C:112 , TYR C:113 , TYR C:147 , MET C:149 , TRP C:159 , ILE C:171 , HIS C:174 , GLY C:178 , ARG C:179 , TYR C:181 , ALA C:182 , VAL C:185 , GLN C:187 , TRP C:200 , ILE C:215 , MET C:219 , SER C:225 , PHE C:231 , HOH C:403 , HOH C:410 , HOH C:453binding site for residue FEC C 302
09AC9SOFTWAREGLU C:86 , ILE D:63 , LEU D:64 , GLY D:65 , ALA D:68 , HOH D:424binding site for residue NA D 301
10AD1SOFTWARESER D:111 , TYR D:113 , LEU D:114 , ARG D:133 , TYR D:147 , MET D:149 , LYS D:151 , TRP D:159 , ILE D:171 , HIS D:174 , GLY D:178 , ARG D:179 , VAL D:185 , GLN D:186 , GLN D:187 , TRP D:200 , ILE D:215 , VAL D:216 , MET D:219 , SER D:225 , PHE D:231 , HOH D:404 , HOH D:406 , HOH D:422 , HOH D:454 , HOH D:484binding site for residue FEC D 302
11AD2SOFTWAREASN C:87 , GLN D:244 , LYS D:247binding site for residue MPD D 303
12AD3SOFTWAREGLU D:86 , ILE E:63 , LEU E:64 , GLY E:65 , ALA E:68 , HOH E:415binding site for residue NA E 301
13AD4SOFTWARESER E:111 , TYR E:113 , TYR E:147 , MET E:149 , TRP E:159 , HIS E:174 , GLY E:178 , ARG E:179 , TYR E:181 , ALA E:182 , VAL E:185 , GLN E:187 , TRP E:200 , ILE E:215 , MET E:219 , SER E:225 , PHE E:231 , HOH E:402 , HOH E:417 , HOH E:469binding site for residue FEC E 302
14AD5SOFTWAREGLN B:244 , LEU B:248 , GLU E:84 , ASN E:87 , HOH E:414 , HOH E:448binding site for residue MPD E 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LOQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LOQ)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee...........hhhhhhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhh.eee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5loq A   4 AVKTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSNYLASHMAGGDDPYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI 251
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee...hhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhhh....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5loq B   6 KTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI 251
                                    15        25        35        45        55        65        75        85        95       105     ||128       138       148       158       168       178       188       198       208       218       228       238       248   
                                                                                                                                   111|                                                                                                                              
                                                                                                                                    125                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee...hhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5loq C   3 EAVKTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSNYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI 251
                                    12        22        32        42        52        62        72        82        92       102       112||     134       144       154       164       174       184       194       204       214       224       234       244       
                                                                                                                                        113|                                                                                                                             
                                                                                                                                         126                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee...........hhhhhhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5loq D   2 NEAVKTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSNYLASHMAGGDDPYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI 251
                                    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


Chain E from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee....hhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhh.eee...eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5loq E   6 KTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSNYYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI 251
                                    15        25        35        45        55        65        75        85        95       105       126       136       146       156       166       176       186       196       206       216       226       236       246     
                                                                                                                                     113|                                                                                                                              
                                                                                                                                      125
   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 5LOQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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
    FEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5loq)
 

(-) 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
  5loq
    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
  Y2113_LISMO | Q8Y5F1
    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)
  1.11.1.-
    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
  Y2113_LISMO | Q8Y5F1
    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
        Y2113_LISMO | Q8Y5F1: 4wws

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LOQ)