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 :  SEMET-LABELED PYLC (REMOTE)
 
Authors :  F. Quitterer, A. List, P. Beck, A. Bacher, M. Groll
Date :  01 Jun 12  (Deposition) - 19 Sep 12  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Amino Acid, Biosynthesis Of Pyrrolysine, Isopeptide Bond Formation, Atp-Grasp Fold, Ligase, Atp-Binding, L-Lysine And 3R-Methyl-D- Ornithine, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Quitterer, A. List, P. Beck, A. Bacher, M. Groll
Biosynthesis Of The 22Nd Genetically Encoded Amino Acid Pyrrolysine: Structure And Reaction Mechanism Of Pylc At 1. 5A Resolution.
J. Mol. Biol. V. 424 270 2012
PubMed-ID: 22985965  |  Reference-DOI: 10.1016/J.JMB.2012.09.007

(-) Compounds

Molecule 1 - PYLC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PET28B
    Gene: MBAR_A0837
    Organism Scientific: METHANOSARCINA BARKERI
    Organism Taxid: 269797
    Strain: FUSARO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION
3MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:104 , PHE A:129 , LYS A:131 , GLU A:135 , SER A:136 , SER A:137 , SER A:138 , GLU A:160 , GLU A:161 , TYR A:162 , VAL A:163 , VAL A:167 , ILE A:189 , TYR A:193 , GLU A:227 , ILE A:229 , GLU A:239 , ASP A:241 , ARG A:243 , MG A:403 , MG A:404 , HOH A:509 , HOH A:525 , HOH A:547 , HOH A:564 , HOH A:568 , HOH A:597 , HOH A:612BINDING SITE FOR RESIDUE ATP A 401
2AC2SOFTWAREGLY A:8 , LYS A:10 , ASP A:31 , LYS A:32 , PHE A:48 , ASP A:49 , VAL A:50 , ILE A:51 , ASN A:71 , GLU A:72 , ASN A:73 , CYS A:76 , HOH A:552 , HOH A:559 , HOH A:616 , HOH A:680BINDING SITE FOR RESIDUE ATP A 402
3AC3SOFTWAREGLU A:227 , GLU A:239 , ATP A:401 , MG A:404 , HOH A:547BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREGLU A:239 , ASP A:241 , ATP A:401 , MG A:403 , HOH A:568BINDING SITE FOR RESIDUE MG A 404
5AC5SOFTWARESER A:169 , GLU A:171 , LYS A:183 , THR A:185 , THR A:248BINDING SITE FOR RESIDUE MG A 405
6AC6SOFTWARESER A:101 , GLU A:239 , ILE A:240 , ASP A:241 , HOH A:534 , HOH A:543BINDING SITE FOR RESIDUE MG A 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:126 -Pro A:127
2Leu A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FFR)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee............eeee.....hhhhhhhhh....eeee...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.............eeee..........eee.........eeee....eeeeeeeeee...eee...eeeee.....eeeeee...hhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhh.hhhhhhhhhh..........eeeeeeeee.hhh.eee.hhhhhh...eeeeeeee..eeeeeee....eeeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ffr A   1 mKTICLVGGKLQGFEAAYLSKKAGmKVVLVDKNPQALIRNYADEFYCFDVIKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRISRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYDDKDEPDTLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHmVTPLPANPLFRQISHDLAANLPLKGImDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSSGINLIELLFRAFTDGVEEIENKYCIYEHLmFGENGVLIPVGEQVLSmGSDYGKFYEEPGIEIFLCKGEYPVFTmVFWGKDREETGAKRCKGLSVL 355
                            |       10        20    |   30        40        50        60        70        80        90       100       110       120       130       140       154       164       174       184       194  |    204       214       224       234       244       254       264       274||     288 |     298       308       318       328     | 338       348       
                            |                      25-MSE                                                                                                                     149|                                        197-MSE                    224-MSE                                            275|       290-MSE          307-MSE                    334-MSE                 
                            1-MSE                                                                                                                                              154                                                                                                                       280
   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 4FFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Leu A:218 - Pro A:219   [ RasMol ]  
    Pro A:126 - Pro A:127   [ 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
  4ffr
    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
  Q46E79_METBF | Q46E79
    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
  Q46E79_METBF | Q46E79
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q46E79_METBF | Q46E79: 4ffl 4ffm 4ffn 4ffo 4ffp

(-) Related Entries Specified in the PDB File

2yzg CRYSTAL STRUCTURE OF D-ALA:D-ALA LIGASE FROM THERMUS THERMOPHILUS HB8
3ouz CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE-ADP COMPLEX FROM CAMPYLOBACTER JEJUNI
4ffl
4ffm
4ffn
4ffo
4ffp