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 :  PLMKR1-KETOREDUCTASE FROM THE FIRST MODULE OF PHOSLACTOMYCIN BIOSYNTHESIS IN STREPTOMYCES SP. HK803
 
Authors :  J. R. Whicher, J. L. Smith
Date :  12 Nov 12  (Deposition) - 10 Jul 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Short Chain Dehydrogenase/Reductase, Ketoreductase, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Bonnett, J. R. Whicher, K. Papireddy, G. Florova, J. L. Smith, K. A. Reynolds
Structural And Stereochemical Analysis Of A Modular Polyketide Synthase Ketoreductase Domain Required For The Generation Of A Cis-Alkene.
Chem. Biol. V. 20 772 2013
PubMed-ID: 23790488  |  Reference-DOI: 10.1016/J.CHEMBIOL.2013.04.014

(-) Compounds

Molecule 1 - PLM1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PMCSG7
    Fragment: UNP RESIDUES 1811-2248
    Gene: PLM1
    Organism Scientific: STREPTOMYCES SP. HK803
    Organism Taxid: 244967

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACA1Ligand/Ion6-AMINOHEXANOIC ACID
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACA-1Ligand/Ion6-AMINOHEXANOIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACA1Ligand/Ion6-AMINOHEXANOIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:191 , GLY A:194 , GLY A:195 , LEU A:196 , SER A:217 , ARG A:218 , GLN A:219 , VAL A:245 , ASP A:246 , VAL A:247 , ALA A:273 , ALA A:274 , GLY A:275 , ALA A:296 , LYS A:297 , SER A:318 , TYR A:332 , TRP A:358 , GLY A:359 , PRO A:360 , TRP A:361 , GLY A:365 , MET A:366 , LEU A:367 , HOH A:601 , HOH A:620 , HOH A:710 , HOH A:766 , HOH A:826 , HOH A:872 , HOH A:910 , HOH A:911 , HOH A:957BINDING SITE FOR RESIDUE NDP A 501
2AC2SOFTWAREGLY B:191 , GLY B:194 , GLY B:195 , LEU B:196 , SER B:217 , ARG B:218 , GLN B:219 , VAL B:245 , ASP B:246 , VAL B:247 , ALA B:273 , ALA B:274 , GLY B:275 , ALA B:296 , LYS B:297 , SER B:318 , TYR B:332 , TRP B:358 , GLY B:359 , PRO B:360 , TRP B:361 , GLY B:365 , MET B:366 , LEU B:367 , ACA B:502 , HOH B:602 , HOH B:618 , HOH B:685 , HOH B:726 , HOH B:831 , HOH B:838 , HOH B:845 , HOH B:957 , HOH B:990BINDING SITE FOR RESIDUE NDP B 501
3AC3SOFTWAREVAL B:277 , SER B:319 , GLN B:329 , TYR B:332 , MET B:366 , LEU B:367 , ASP B:371 , NDP B:501 , HOH B:913 , HOH B:915 , HOH B:987 , HOH B:1019BINDING SITE FOR RESIDUE ACA B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HXY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HXY)

(-) 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:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..........eeeee..hhhhhh..................eeeee..hhhhhhhhhhhhh......eeeeee.............hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhh...eeeee..eeeeeeeee.............eeeee...hhhhhhhhhhhhhhh...eeeeee.hhhhh.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhh.ee..hhhhhhhhhhhhhhh......eeeeehhhhhhhhhh....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hxy A   1 RTGWFSETWRQLGTADRVPGNWLLLGEVPPALGSLFDDPLTAASWDRSTAPDGVLVGAGAAEDLLAALHEVAGHPTGPVWCVTSRAVGVGTVDDPAADVRAAGVWGLGRVAGLELPDRWGGLVDLPERIDDATRRALAGTLTDGEDQLAVRDGQLWARRLVTTPAPQTGTWTPKGTVLITGGTGGLGGHVARRVAEQGSADRILLLSRQGSAAPGATELLEGIRAFGATAEAVAVDVTDRAAMSGLIDALAAEGAPVRTVVHAAGVVRDVRIAETGAEELAAQMAAKVEGALLLDELLPDLDDFVLFSSISGIWGAAGQAGYAAGNACLDALARRRREQGKRAVSVAWGPWAGGGMLTEHDERELRKRGLTPLLVPAALQAMEQAIMSDRAGDPVVADVTWSRFLPAFTASRPSPLFGSFEEKAA 435
                                    10  ||    23        33        43        53        63        73        83        93       103       113       123       133       143  ||   160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430     
                                       13|                                                                                                                              146|                                                                                                                                                                                                                                                                                         
                                        17                                                                                                                               154                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee..........eeeee..hhhhhh..................eeeee..hhhhhhhhhhhhh......eeeeee....hhhhh....hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhh....eeeee..eeeeeeeee.............eeeee...hhhhhhhhhhhhhhh...eeeeee.hhhhh.hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhh.ee..hhhhhhhhhhhhhhh......eeeeehhhhhhhhhh....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hxy B   0 ARTGWFSETWRQLGRAATADRVPGNWLLLGEVPPALGSLFDDPLTAASWDRSTAPDGVLVGAGAAEDLLAALHEVAGHPTGPVWCVTSRAVGVGTVDDPAADVRAAGVWGLGRVAGLELPDRWGGLVDLPERIDDATRRALAGTLTDDGEDQLAVRDGQLWARRLVTTPAPQTGTWTPKGTVLITGGTGGLGGHVARRVAEQGSADRILLLSRQGSAAPGATELLEGIRAFGATAEAVAVDVTDRAAMSGLIDALAAEGAPVRTVVHAAGVVRDVRIAETGAEELAAQMAAKVEGALLLDELLPDLDDFVLFSSISGIWGAAGQAGYAAGNACLDALARRRREQGKRAVSVAWGPWAGGGMLTEHDERELRKRGLTPLLVPAALQAMEQAIMSDRAGDPVVADVTWSRFLPAFTASRPSPLFGSFEEKAA 435
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139      |155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435
                                                                                                                                                                            146|                                                                                                                                                                                                                                                                                          
                                                                                                                                                                             153
   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 4HXY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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
    ACA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hxy)
 
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
  4hxy
    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
  Q6V1M8_9ACTN | Q6V1M8
    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
  Q6V1M8_9ACTN | Q6V1M8
    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 4HXY)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HXY)