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 :  CRYSTAL STRUCTURE OF SEMET-SUBSTITUTED CURJ CARBON METHYLTRANSFERASE
 
Authors :  M. A. Skiba, J. L. Smith
Date :  30 Sep 16  (Deposition) - 19 Oct 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, Transferase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Skiba, A. P. Sikkema, W. D. Fiers, W. H. Gerwick, D. H. Sherman, C. C. Aldrich, J. L. Smith
Domain Organization And Active Site Architecture Of A Polyketide Synthase C-Methyltransferase.
Acs Chem. Biol. V. 11 3319 2016
PubMed-ID: 27723289  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00759

(-) Compounds

Molecule 1 - CURJ
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1269-1649
    Gene: LYNGBM3L_74460
    Organism Scientific: MOOREA PRODUCENS 3L
    Organism Taxid: 489825
    Synonym: POLYKETIDE SYNTHASE MODULE

 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  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GDS1Ligand/IonOXIDIZED GLUTATHIONE DISULFIDE
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GDS-1Ligand/IonOXIDIZED GLUTATHIONE DISULFIDE
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1GDS1Ligand/IonOXIDIZED GLUTATHIONE DISULFIDE
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:169 , GLY A:205 , ALA A:206 , GLY A:207 , THR A:208 , GLY A:209 , GLY A:210 , THR A:211 , ASP A:230 , ILE A:231 , PHE A:235 , LEU A:254 , ASP A:255 , ILE A:256 , GLU A:257 , ALA A:276 , ASN A:277 , VAL A:278 , HOH A:634 , HOH A:654 , HOH A:677binding site for residue SAH A 501
2AC2SOFTWARETYR B:169 , GLY B:205 , ALA B:206 , GLY B:207 , THR B:208 , GLY B:209 , GLY B:210 , THR B:211 , ASP B:230 , ILE B:231 , PHE B:235 , LEU B:254 , ASP B:255 , ILE B:256 , GLU B:257 , ALA B:276 , ASN B:277 , VAL B:278 , HOH B:614 , HOH B:618 , HOH B:657 , HOH B:687binding site for residue SAH B 501
3AC3SOFTWAREGLU B:41 , ASP B:45 , ILE B:95 , LYS B:107 , THR B:108 , GLN B:110 , VAL B:112 , ARG B:197binding site for residue GDS B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:359 -Pro A:360
2Leu B:359 -Pro B:360

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5THY)

(-) 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeehhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeee..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee......hhhhhhhhh....eeeeeee.hhhhhhhhhhhh.....eeeee.....hhhhhh.....eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhhhhhhhh.............hhhhhhhhhhhh.eeeeeee......hhhhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5thy A  -5 YFQSNALPPDFLLDPVEVSQQLAPSLTELVTLLDNARTSEIGTQLEELSVDYIVQGLLQmGWSYQPTESFDLDAAAQCLGVVPTQVRLFERLLQILAEVGILQSNQQQWQVQKTAQKVNPSKQSQSLLSQYPDEAATLTLLERCASQLSGVLRGEIDPVQLVFPQGDLTTATQLYKDSAVAKVmNTIVEKVImKAmEKLPPSRGIRLLEIGAGTGGTTSYILPHLNPNQTEYIFTDIGALFTSKAQEKFQDYRFLGYQTLDIEVDPSSQGFESHRYDVIIAANVLHATTSLKQTLSHVRQLLAPGGILVLYEATTRSRWVDLIFGLLEGWWKFTDYELRPDYPLLNREQWKKVLSETGFTQVVTLPEVEGmAEALSQQTVIVAQAAS 381
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   |   184  |  | 194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364|      374       
                                                                                      54-MSE                                                                                                                     178-MSE  187-MSE                                                                                                                                                                           365-MSE            
                                                                                                                                                                                                                             190-MSE                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeehhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeee..eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee......hhhhhhhhh....eeeeeee.hhhhhhhhhhhh.....eeeee.....hhhhh......eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhhhhhhhh.............hhhhhhhhhhhh.eeeeeee......hhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5thy B   6 LLDPVEVSQQLAPSLTELVTLLDNARTSEIGTQLEELSVDYIVQGLLQmGWSYQPTESFDLDAAAQCLGVVPTQVRLFERLLQILAEVGILQSNQQQWQVQKTAQKVNPSKQSQSLLSQYPDEAATLTLLERCASQLSGVLRGEIDPVQLVFPQGDLTTATQLYKDSAVAKVmNTIVEKVImKAmEKLPPSRGIRLLEIGAGTGGTTSYILPHLNPNQTEYIFTDIGALFTSKAQEKFQDYRFLGYQTLDIEVDPSSQGFESHRYDVIIAANVLHATTSLKQTLSHVRQLLAPGGILVLYEATTRSRWVDLIFGLLEGWWKFTDYELRPDYPLLNREQWKKVLSETGFTQVVTLPEVEGmAEALSQQTVIVAQAAS 381
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175  |    185 |  |  195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375      
                                                                           54-MSE                                                                                                                     178-MSE  187-MSE                                                                                                                                                                           365-MSE            
                                                                                                                                                                                                                  190-MSE
   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 5THY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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
    GDS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:359 - Pro A:360   [ RasMol ]  
    Leu B:359 - Pro B:360   [ RasMol ]  
 
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
  5thy
    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
  F4Y426_9CYAN | F4Y426
    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
  F4Y426_9CYAN | F4Y426
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        F4Y426_9CYAN | F4Y426: 5thz 5tz6

(-) Related Entries Specified in the PDB File

5thz