Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE 2.2 A CRYSTAL STRUCTURE OF CYP109E1 FROM BACILLUS MEGATERIUM BOUND WITH FOUR CORTICOSTERONE MOLECULES
 
Authors :  I. K. Jozwik, A. M. W. H. Thunnissen
Date :  09 Jun 16  (Deposition) - 05 Oct 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bacillus, Bacterial Proteins, Binding Sites, Catalysis, Corticosterone, Cytochrome P-450 Enzyme System, Cytochrome P450, Hydroxylation, Escherichia Coli, Heme, Ligands, Molecular Structure, Oxidation-Reduction, Oxygen, Protein, Protein Structure, Secondary, Steroids, Substrate Specificity, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. K. Jozwik, F. M. Kiss, A. Abdulmughni, E. Brill, J. Zapp, J. Pleiss, R. Bernhardt, A. W. Thunnissen
Structural Basis Of Steroid Binding And Oxidation By The Cytochrome P450 Cyp109E1 From Bacillus Megaterium.
Febs J. V. 283 4128 2016
PubMed-ID: 27686671  |  Reference-DOI: 10.1111/FEBS.13911

(-) Compounds

Molecule 1 - CYTOCHROME P450
    Chains: A, B
    EC Number: 1.14.14.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C43
    Gene: BMD_3874
    Organism Scientific: BACILLUS MEGATERIUM (STRAIN DSM 319)
    Organism Taxid: 592022
    Strain: DSM 319

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1C0R8Ligand/IonCORTICOSTERONE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1C0R4Ligand/IonCORTICOSTERONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1C0R4Ligand/IonCORTICOSTERONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:84 , ILE A:85 , HIS A:92 , ARG A:96 , LEU A:239 , ALA A:242 , GLY A:243 , THR A:246 , THR A:247 , LEU A:250 , LEU A:292 , ARG A:294 , ALA A:344 , PHE A:345 , GLY A:346 , ILE A:349 , HIS A:350 , CYS A:352 , GLY A:354 , LEU A:357 , ALA A:358 , C0R A:502 , HOH A:610 , HOH A:616 , HOH A:622 , HOH A:648binding site for residue HEM A 501
02AC2SOFTWAREILE A:85 , ILE A:168 , VAL A:169 , LYS A:187 , ILE A:241 , GLU A:245 , VAL A:289 , LEU A:292 , VAL A:392 , HEM A:501 , C0R A:503 , C0R A:504 , C0R A:505 , HOH A:622 , HOH A:707 , ARG B:177 , GLU B:178binding site for residue C0R A 502
03AC3SOFTWAREARG A:69 , PRO A:71 , GLN A:75 , ASN A:86 , ILE A:241 , C0R A:502 , C0R A:504 , C0R A:505 , GLU B:181 , GLN B:185binding site for residue C0R A 503
04AC4SOFTWAREARG A:44 , VAL A:46 , ARG A:69 , LEU A:292 , HIS A:293 , HIS A:312 , PHE A:391 , C0R A:502 , C0R A:503 , C0R A:505 , HOH A:610 , LYS B:182binding site for residue C0R A 504
05AC5SOFTWAREARG A:76 , GLN A:184 , MET A:188 , ASN A:191 , C0R A:502 , C0R A:503 , C0R A:504 , GLU B:181binding site for residue C0R A 505
06AC6SOFTWARELEU B:84 , ILE B:85 , HIS B:92 , ARG B:96 , LEU B:239 , GLY B:243 , THR B:246 , THR B:247 , LEU B:292 , ARG B:294 , ALA B:344 , PHE B:345 , GLY B:346 , ILE B:349 , HIS B:350 , CYS B:352 , GLY B:354 , ALA B:358 , C0R B:502 , HOH B:610 , HOH B:626 , HOH B:630binding site for residue HEM B 501
07AC7SOFTWAREARG A:177 , ILE B:85 , ILE B:168 , VAL B:169 , LYS B:187 , ILE B:241 , GLU B:245 , THR B:246 , VAL B:289 , LEU B:292 , VAL B:392 , HEM B:501 , C0R B:503 , C0R B:504 , C0R B:505 , HOH B:610 , HOH B:653binding site for residue C0R B 502
08AC8SOFTWAREGLU A:181 , GLN A:185 , ARG B:69 , PRO B:71 , GLN B:75 , LEU B:80 , GLY B:81 , ASN B:86 , ILE B:241 , C0R B:502 , C0R B:504 , C0R B:505 , HOH B:650binding site for residue C0R B 503
09AC9SOFTWARELYS A:182 , ARG B:44 , VAL B:46 , ARG B:69 , LEU B:292 , HIS B:293 , HIS B:312 , PHE B:391 , C0R B:502 , C0R B:503 , C0R B:505binding site for residue C0R B 504
10AD1SOFTWAREGLU A:181 , ARG B:76 , MET B:188 , ASN B:191 , C0R B:502 , C0R B:503 , C0R B:504binding site for residue C0R B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L91)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:89 -Pro A:90
2Lys A:338 -Pro A:339
3Pro B:89 -Pro B:90
4Lys B:338 -Pro B:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L91)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L91)

(-) Exons   (0, 0)

(no "Exon" information available for 5L91)

(-) Sequences/Alignments

Asymmetric 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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhhhhh.eeee....eeee.hhhhhhhhhhh...ee............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee....................eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l91 A  17 QTKEERFNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDRRPPQNQRQTALGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVAGPSNNERETLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNVHHH 407
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406 


Chain B from PDB  Type:PROTEIN  Length:389
                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhh.eeee....eeee.hhhhhhhhhhh...ee............hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee....................eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l91 B  18 TKEERFNPFSWYEEMRNTAPVQWDEERQVWDVFHYDGVKEVLEQKNIFSSDRRPPQNQRQTALGTSLINIDPPKHAEMRALVNKAFTPKAMKAWEPKIARITNELLQEVEHLEDIDIVEHLSYPLPVMVIADILGVPIEDQRQFKDWSDIIVAGPSNNERETLEKLQQEKMKANDELETYFYRIIEEKRTRPGDDIISVLLQAKEEGKQLTDEEIVGFSILLLIAGNETTTNLISNTIYCLMEDKASFERLKREKELLPSGIEEVLRYRSPVQALHRIVKEDVTLAGKKLKAGEHVVPWMGSAHRDAEYFEDPEVFKIDRKPNVHMAFGRGIHFCLGAPLARIEAKIMLAELIDRYPQMDWSPSFELKPIESTFVYGLKELLIRKNVHH 406
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397
   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 5L91)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L91)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L91)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    C0R  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ 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 ]
 
  Cis Peptide Bonds
    Lys A:338 - Pro A:339   [ RasMol ]  
    Lys B:338 - Pro B:339   [ RasMol ]  
    Pro A:89 - Pro A:90   [ RasMol ]  
    Pro B:89 - Pro B:90   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5l91
    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
  D5DKI8_BACMD | D5DKI8
    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)
  1.14.14.-
    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
  D5DKI8_BACMD | D5DKI8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D5DKI8_BACMD | D5DKI8: 5l90 5l92 5l94

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L91)