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 THE LNMZ CYTOCHROME P450 HYDROXYLASE FROM THE LEINAMYCIN BIOSYNTHETIC PATHWAY OF STREPTOMYCES ATROOLIVACEUS S-140 AT 1.8 A RESOLUTION
 
Authors :  M. Ma, J. Lohman, J. Rudolf, M. D. Miller, H. Cao, J. Osipiuk, A. Joachimi G. N. Phillips Jr. , B. Shen, Midwest Center For Structural Genom (Mcsg), Enzyme Discovery For Natural Product Biosynthesis (N
Date :  02 Apr 15  (Deposition) - 12 Aug 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydroxylase, Leinamycin, Heme, Monooxygenase, Oxidoreductase, Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Enzyme Discovery For Natural Product Biosynthesis, Natpro (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ma, J. Lohman, J. Rudolf, M. D. Miller, H. Cao, J. Osipiuk, A. Joachimiak, G. N. Phillips Jr. , B. Shen
Crystal Structure Of The Lnmz Cytochrome P450 Hydroxylase From The Leinamycin Biosynthetic Pathway Of Streptomyces Atroolivaceus S-140
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOCHROME P450 HYDROXYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSF-TEV/LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LNMZ
    Organism Scientific: STREPTOMYCES ATROOLIVACEUS
    Organism Taxid: 66869
    Strain: S-140

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CL2Ligand/IonCHLORIDE ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MG3Ligand/IonMAGNESIUM ION
5P331Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:89 , LEU A:90 , HIS A:97 , ARG A:101 , PHE A:108 , ILE A:237 , GLY A:240 , GLY A:241 , THR A:244 , ILE A:291 , SER A:292 , ARG A:294 , VAL A:344 , PHE A:345 , GLY A:346 , HIS A:350 , CYS A:352 , GLY A:354 , LEU A:357 , ALA A:358 , P33 A:407 , HOH A:409 , HOH A:422binding site for residue HEM A 401
2AC2SOFTWAREASP A:64 , ASP A:163 , HOH A:544 , HOH A:545 , HOH A:546 , HOH A:547binding site for residue MG A 402
3AC3SOFTWAREASP A:198 , HOH A:548 , HOH A:549 , HOH A:550 , HOH A:551 , HOH A:552binding site for residue MG A 403
4AC4SOFTWAREGLU A:271 , HOH A:553 , HOH A:554 , HOH A:555 , HOH A:556 , HOH A:557binding site for residue MG A 404
5AC5SOFTWAREHIS A:351 , ARG A:359binding site for residue CL A 405
6AC6SOFTWAREGLN A:187 , ARG A:308 , MET A:373 , PRO A:374 , GLY A:375 , TRP A:400binding site for residue CL A 406
7AC7SOFTWAREGLU A:87 , PRO A:228 , GLY A:232 , SER A:236 , GLY A:240 , THR A:244 , ALA A:268 , GLY A:290 , HEM A:401 , HOH A:409 , HOH A:537binding site for residue P33 A 407
8AC8SOFTWARETYR A:55 , HIS A:342 , HIS A:347 , GLY A:348 , HIS A:351binding site for residue 1PE A 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z5Q)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:15 -Pro A:16
2Pro A:94 -Pro A:95
3Ala A:136 -Pro A:137
4Gly A:178 -Glu A:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z5Q)

(-) 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee......eeee.hhhhhhhhhhh..eehhhhhhh............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...eeee......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z5q A  10 PAPVAYPFDGDPIRVQLPFGEPAWLVTRYDDARFVLTDRRFSRHLATQRDEPRMTPRAVPESILTMDPPDHTRLRTLVSKAFTPRRIESKRAWIGELAAGLVADMKAGGAPAELVGSYALAIPVTVICELLGVPEDDRTRLRGWCDAALSTGELTDEECVQSFMDLQKYFEDLVKERRAEPRDDLTSALIEARDAHDRLAEPELIGLCISILIGGFETTASEISSFVHVLQQRRELWTRLCADPEAIPAAVEELLRFVPFAANGISPRYALEDMTVGGVLVREGEPVIVDTSAVNRDGLVFDNADEVVIDRADNRHMVFGHGAHHCLGAHLARVELQEALKALVEGMPGLRLSGDAPRVMHVEW 400
                                   |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    || 396    
                                  17|                                                                                                                                                                                                                                                                                                                                                       381|        
                                   35                                                                                                                                                                                                                                                                                                                                                        392
   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 4Z5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z5Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z5Q)

(-) Gene Ontology  (7, 7)

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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P33  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:136 - Pro A:137   [ RasMol ]  
    Gly A:178 - Glu A:179   [ RasMol ]  
    Pro A:94 - Pro A:95   [ RasMol ]  
    Tyr A:15 - Pro A: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 | 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
  4z5q
    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
  Q8GGM6_STRAZ | Q8GGM6
    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)
  (no 'Enzyme Classificator' available)
    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
  Q8GGM6_STRAZ | Q8GGM6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4Z5Q)

(-) Related Entries Specified in the PDB File

4z5p