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 :  POLYETHYLENE 600-BOUND FORM OF P450 CYP125A3 MUTANT FROM MYOBACTERIUM SMEGMATIS - W83Y
 
Authors :  P. J. Ortiz De Montellano, D. J. Frank, C. A. Waddling
Date :  15 Sep 15  (Deposition) - 18 Nov 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Cholesterol Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Frank, C. A. Waddling, M. La, P. R. Ortiz De Montellano
Cytochrome P450 125A4, The Third Cholesterol C-26 Hydroxylase From Mycobacterium Smegmatis.
Biochemistry V. 54 6909 2015
PubMed-ID: 26522442  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01029

(-) Compounds

Molecule 1 - CYTOCHROME P450 CYP125
    Chains: A
    EC Number: 1.14.13.151
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCW
    Expression System Strain: DH5(ALPHA)
    Expression System Taxid: 668369
    Expression System Vector Type: PLASMID
    Gene: CYP125, MSMEI_5834
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / MC(2)155)
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CIT1Ligand/IonCITRIC ACID
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:79 , LEU A:99 , LEU A:100 , HIS A:107 , ARG A:111 , LEU A:248 , ALA A:251 , GLY A:252 , THR A:255 , THR A:256 , PHE A:299 , ARG A:301 , TYR A:324 , GLY A:351 , PHE A:352 , GLY A:353 , GLY A:354 , ALA A:357 , HIS A:358 , TYR A:359 , CYS A:360 , ILE A:361 , GLY A:362 , LEU A:365 , ALA A:366 , 1PE A:505 , HOH A:602 , HOH A:604 , HOH A:635binding site for residue HEM A 501
2AC2SOFTWAREVAL A:82 , PRO A:84 , GLY A:186 , GLU A:187 , SER A:395 , GLY A:396 , TRP A:397 , HOH A:669binding site for residue PO4 A 502
3AC3SOFTWARECYS A:155 , ASN A:181binding site for residue PO4 A 503
4AC4SOFTWARELEU A:94 , ARG A:96 , ALA A:97 , MET A:208 , GLU A:212 , ASP A:238binding site for residue CIT A 504
5AC5SOFTWAREILE A:80 , GLN A:95 , LEU A:100 , VAL A:250 , ALA A:251 , HEM A:501binding site for residue 1PE A 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:104 -Pro A:105
2Ser A:345 -Pro A:346

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DQN)

(-) 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:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhh.hhhhhhhhhhhh.eeeee...........eeeee.hhhhhhhhhhh...ee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhh.................................hhhhhhhhhhhhhhhhhhhh...ee....ee........eee.eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dqn A   2 PTPNIPSDFDFLDATLNLERLPVEELAELRKSEPIHWVDVPGGTGGFGDKGYWLVTKHADVKEVSRRSDVFGSSPDGAIPVYPQDMTREAVDLQRAVLLNMDAPQHTRLRKIISRGFTPRAIGRLEDELRSRAQKIAQTAAAQGAGDFVEQVSCELPLQAIAELLGVPQDDRDKLFRWSNEMTAGEDPEYADVDPAMSSFELISYAMKMAEERAVNPTEDIVTKLIEADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITHGMIAFAQNPDQWELYKKERPETAADEIVRWATPVSAFQRTALEDVELGGVQIKKGQRVVMSYRSANFDEEVFEDPHTFNILRSPNPHVGFGGTGAHYCIGANLARMTINLIFNAIADNMPDLKPIGAPERLKSGWLNGIKHWQVDYTGA 411
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
   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 5DQN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 14)

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 ]
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:104 - Pro A:105   [ RasMol ]  
    Ser A:345 - Pro A:346   [ 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
  5dqn
    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
  CP125_MYCS2 | A0R4Y3
    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)
  1.14.13.151
    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
  CP125_MYCS2 | A0R4Y3
    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
        CP125_MYCS2 | A0R4Y3: 4apy

(-) Related Entries Specified in the PDB File

4apy 4APY IS THE NATIVE FORM OF THIS PROTEIN