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
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)

(-) Description

Title :  CMLA BETA-HYDROXYLASE IN CHEMICALLY REDUCED DIFERROUS STATE
 
Authors :  C. J. Knoot, J. D. Lipscomb
Date :  16 Jun 16  (Deposition) - 26 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxygen Activation, Diiron Cluster, Antibiotic Biosynthesis, Beta- Hydroxylase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Jasniewski, C. J. Knoot, J. D. Lipscomb, L. Que
A Carboxylate Shift Regulates Dioxygen Activation By The Diiron Nonheme Beta-Hydroxylase Cmla Upon Binding Of A Substrate-Loaded Nonribosomal Peptide Synthetase.
Biochemistry V. 55 5818 2016
PubMed-ID: 27668828  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00834

(-) Compounds

Molecule 1 - CMLA PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Gene: SVEN_0921
    Organism Scientific: STREPTOMYCES VENEZUELAE (STRAIN ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)
    Organism Taxid: 953739
    Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2GOL2Ligand/IonGLYCEROL
3K1Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL4Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:305 , HIS A:307 , GLU A:377 , ASP A:403 , FE A:602 , HOH A:776binding site for residue FE A 601
2AC2SOFTWAREASP A:309 , HIS A:310 , ASP A:403 , FE A:601 , HOH A:740 , HOH A:776 , HOH A:865binding site for residue FE A 602
3AC3SOFTWARETYR A:148 , SER A:150 , TYR A:153 , HOH A:868binding site for residue K A 603
4AC4SOFTWAREASP A:198 , ARG A:320 , PHE A:350 , THR A:351 , HOH A:738 , HOH A:782binding site for residue GOL A 604
5AC5SOFTWAREALA A:121 , ALA A:122 , ARG A:126 , GLU A:151 , TYR A:152 , HOH A:742binding site for residue GOL A 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KIK)

(-) 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:521
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh........eeeee......eeeeehhhhhhhh...hhh.eeeeeee.....................eeee....hhhhhhhhhh.eehhhhhhhhhhh..hhhhhhhhhh.eee.....eeeeee..eeeeee..eeeee.................hhhhh...eeeee.........hhhhhhhhh..eeeeeee..........hhhhhhhhh....eeee....eeee..eeeeee...............eeeeee..eeeee.........hhhhhhhhhhh...eeeee......hhhhhhhhhh....hhhhhhh......hhhhhhhhhhhhh..eeeee....hhhhhhh........hhhhhhhhhhhhhhhh...eeee....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kik A  -1 HMRYSLRQDIAVEPVIAGWYGWSYLLPPQTLARFVHNRFNRIVESYLDDPQVHAAAVRQRRMHGGPWIHAHEHRDAIEAWYRETAPRRERLDELFEAVRRLEEDILPRHHGECLDPVYQELPAALAGRVEVFYGRDNRTADYRFVEPLMYASEYYDESWQQVRFRPVTEDAREFALTTPMLEYGPEQLLVNVPLNSPLLDAVFRGGLTGTELDDLAARFGLDGERAARFASYFEPTPEEDVLEYVGHACVFARHRGTTFLVDPVLSYSGYPGGAENRFTFADLPERIDHLLITHNHQDHMLFETLLRIRHRVGRVLVPKSTNASLVDPGLGGILRRLGFTDVVEVDDLETLSCGSAEVVALPFLGEHGDLRIRSKTGWLIRFGERSVLFAADSTNISPTMYTKVAEVIGPVDTVFIGMESIGAAASWIYGPLYGEPLDRRTDQSRRLNGSNFPQAREIVDALEPDEVYVYAMGLEPWMGVVMAVDYDESHPAIVDSDLLVRHVQDKGGTAERLHLRRTLRL 532
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      |251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531 
                                                                                                                                                                                                                                                                      235|                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                       249
   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 5KIK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ 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
(no "Cis Peptide Bonds" information available for 5kik)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5kik
    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
  F2RB80_STRVP | F2RB80
    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)
  (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
  F2RB80_STRVP | F2RB80
    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
        F2RB80_STRVP | F2RB80: 5kil
UniProtKB/TrEMBL
        F2RB80_STRVP | F2RB80: 4jo0

(-) Related Entries Specified in the PDB File

4jo0 4JO0 IS THIS SAME ENZYME IN OXIDIZED CLUSTER STATE
5kil