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 ASP251GLY/GLN307HIS MUTANT OF CYTOCHROME P450 BM3
 
Authors :  G. Di Nardo, V. Dell'Angelo, G. Gilardi
Date :  25 Sep 15  (Deposition) - 20 Jan 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Cytochrome P450, Random Mutagenesis, Drug Metabolism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Di Nardo, V. Dell'Angelo, G. Catucci, S. J. Sadeghi, G. Gilardi
Subtle Structural Changes In The Asp251Gly/Gln307His P450 Bm3 Mutant Responsible For New Activity Toward Diclofenac, Tolbutamide And Ibuprofen.
Arch. Biochem. Biophys. V. 602 106 2016
PubMed-ID: 26718083  |  Reference-DOI: 10.1016/J.ABB.2015.12.005

(-) Compounds

Molecule 1 - BIFUNCTIONAL P-450/NADPH-P450 REDUCTASE
    Chains: A, C
    EC Number: 1.14.14.1, 1.6.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CYP102A1, CYP102
    Mutation: YES
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Synonym: CYTOCHROME P450(BM-3),CYTOCHROME P450BM-3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:69 , LEU A:86 , PHE A:87 , TRP A:96 , ILE A:153 , ALA A:264 , GLY A:265 , THR A:268 , THR A:269 , THR A:327 , ALA A:328 , PHE A:331 , PRO A:392 , PHE A:393 , GLY A:394 , ARG A:398 , ALA A:399 , CYS A:400 , ILE A:401 , GLY A:402 , ALA A:406 , HOH A:616 , HOH A:635 , HOH A:637 , HOH A:670binding site for residue HEM A 501
2AC2SOFTWARELYS C:69 , LEU C:86 , PHE C:87 , TRP C:96 , ALA C:264 , GLY C:265 , THR C:268 , THR C:269 , LEU C:272 , THR C:327 , ALA C:328 , PHE C:331 , PRO C:392 , PHE C:393 , GLY C:394 , ARG C:398 , CYS C:400 , ILE C:401 , GLY C:402 , ALA C:406 , HOH C:613 , HOH C:616 , HOH C:620 , HOH C:640binding site for residue HEM C 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DYP)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eee..hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhh..............hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dyp A   2 IKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLNKRQFQEDIKVMNDLVDKIIADRKASQSDDLLTHMLNGKDPETGEPLDGENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKHVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL 455
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      |203       213       223  ||   235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455
                                                                                                                                                                                                                    188|                      226|                                                                                                                                                                                                                                  
                                                                                                                                                                                                                     201                       229                                                                                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eee..hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhh..............hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dyp C   1 TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASQSDDLLTHMLNGKDPETGEPLDGENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKHVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLG 456
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       194       204       214       224 ||    236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456
                                                                                                                                                                                                                      189|                             226|                                                                                                                                                                                                                                   
                                                                                                                                                                                                                       194                              229
   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 5DYP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dyp)
 

(-) 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
  5dyp
    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
  CPXB_BACMB | P14779
    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)
  1.14.14.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.6.2.4
    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
  CPXB_BACMB | P14779
    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
        CPXB_BACMB | P14779: 1bu7 1bvy 1fag 1fah 1jme 1jpz 1p0v 1p0w 1p0x 1smi 1smj 1yqo 1yqp 1zo4 1zo9 1zoa 2bmh 2hpd 2ij2 2ij3 2ij4 2j1m 2j4s 2nnb 2uwh 2x7y 2x80 3ben 3cbd 3dgi 3ekb 3ekd 3ekf 3hf2 3kx3 3kx4 3kx5 3m4v 3npl 3psx 3wsp 4dqk 4dql 4dtw 4dty 4dtz 4du2 4dua 4dub 4duc 4dud 4due 4duf 4h23 4h24 4hgf 4hgg 4hgh 4hgi 4hgj 4kew 4key 4kf0 4kf2 4kpa 4kpb 4o4p 4rsn 4wg2 4zf6 4zf8 4zfa 4zfb 5b2u 5b2v 5b2w 5b2x 5b2y 5dyz 5e78 5e7y 5e9z 5jq2 5jqu 5jqv 5jtd

(-) Related Entries Specified in the PDB File

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