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 :  PYLC IN COMPLEX WITH PHOSPHORYLATED D-ORNITHINE
 
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 :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Amino Acid, Biosynthesis Of Pyrrolysine, Isopeptide Bond Formation, Atp-Grasp Fold, Ligase, L-Lysine And 3R-Methyl-D-Ornithine, Cytosol, Ligase-Reaction Intermediate Complex (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  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
10TK1Ligand/Ion(2R)-2,5-DIAMINOPENTANOYL DIHYDROGEN PHOSPHATE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:136 , SER A:137 , SER A:169 , GLU A:171 , ASP A:225 , GLU A:227 , GLU A:239 , ASP A:241 , ARG A:243 , SER A:246 , GLN A:247 , THR A:248 , GLU A:302 , ADP A:902 , MG A:903 , MG A:904 , HOH A:1019 , HOH A:1204 , HOH A:1211 , HOH A:1222BINDING SITE FOR RESIDUE 0TK A 901
2AC2SOFTWARELYS 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 , GLU A:227 , ILE A:229 , ILE A:238 , GLU A:239 , 0TK A:901 , MG A:903 , MG A:904 , HOH A:1011 , HOH A:1018 , HOH A:1029 , HOH A:1211 , HOH A:1236BINDING SITE FOR RESIDUE ADP A 902
3AC3SOFTWAREGLU A:227 , GLU A:239 , 0TK A:901 , ADP A:902 , MG A:904 , HOH A:1211BINDING SITE FOR RESIDUE MG A 903
4AC4SOFTWAREGLU A:239 , ASP A:241 , 0TK A:901 , ADP A:902 , MG A:903 , HOH A:1236BINDING SITE FOR RESIDUE MG A 904
5AC5SOFTWAREGLY 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:1036 , HOH A:1097 , HOH A:1178 , HOH A:1218BINDING SITE FOR RESIDUE ATP A 905

(-) SS Bonds  (0, 0)

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

(-) 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 4FFO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FFO)

(-) 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee............eeee.....hhhhhhhhhh...eeee...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.............eeee..........eee.......eeee....eeeeeeeeee...eee...eeeee.....eeeeee...hhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhh.hhhhhhhhhh..........eeeeeeeee.hhh.eee.hhhhhh...eeeeeeee..eeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ffo A   1 MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDVIKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRISRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYGLEPDTLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPLFRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSSGINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSDYGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFGAVL 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    || 156       166       176       186       196       206       216       226       236       246       256       266       280       290       300       310       320       330       340       350       360   
                                                                                                                                                                          145|                                                                                                                        275|                                                                                   
                                                                                                                                                                           152                                                                                                                         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 4FFO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    0TK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
    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
  4ffo
    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 4ffp 4ffr

(-) 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
4ffp
4ffr