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 :  CRYSTAL STRUCTURE OF THE CANDIDA ALBICANS METHIONINE SYNTHASE IN COMPLEX WITH GLUTAMINE
 
Authors :  D. Ubhi, J. D. Robertus
Date :  12 Jun 13  (Deposition) - 05 Mar 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A
Keywords :  Cobalamin-Independent, Surface Entropy Reduction, Fungal, Dual Tim Barrels, Methionine Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Ubhi, G. Kago, A. F. Monzingo, J. D. Robertus
Structural Analysis Of A Fungal Methionine Synthase With Substrates And Inhibitors.
J. Mol. Biol. V. 426 1839 2014
PubMed-ID: 24524835  |  Reference-DOI: 10.1016/J.JMB.2014.02.006

(-) Compounds

Molecule 1 - 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CAO19.10083, CAO19.2551, MET6
    Mutation: YES
    Organism Scientific: CANDIDA ALBICANS SC5314
    Organism Taxid: 237561
    Strain: BWP17
    Synonym: COBALAMIN-INDEPENDENT METHIONINE SYNTHASE, METHIONINE SYNTHASE, VITAMIN-B12 INDEPENDENT ISOZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GLN1Mod. Amino AcidGLUTAMINE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:657 , CYS A:659 , ASP A:738 , CYS A:739 , HOH A:1279BINDING SITE FOR RESIDUE ZN A 801
2AC2SOFTWAREILE A:446 , GLY A:447 , SER A:448 , GLU A:499 , MET A:566 , ASP A:614 , HIS A:657 , CYS A:659 , CYS A:739 , GLY A:740BINDING SITE FOR RESIDUE GLN A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L6O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L6O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L6O)

(-) Exons   (0, 0)

(no "Exon" information available for 4L6O)

(-) 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:747
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhhh..hhhhhh...hhhhhhhhhhhh.......eee......eee..ee.............hhhhhhhhhhhhh....eeeeehhhhhhhh.ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhh.....eeeee...hhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhhh...eeeee..hhhhh..hhhhh...hhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..............hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh..eeee......eeee..eee...eeeeeee.....hhhhhhhhhhh.....eeeeehhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh....hhhhhhhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhh..eeee...hhhhhhhh....eeee.........hhhhhhhhhhhhhhh.hhhhh...........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l6o A   1 MVQSSVLGFPRIGGQRELKKITEAYWSGKATVEELLAKGKELREHNWKLQQKAGVDIIPSNDFSYYDQVLDLSLLFNAIPERYTKFDLAPIDVLFAMGRGLQVTALEMVKWFDSNYHYVRPTFSHSTEFKLNTAAGIKPVDEFNEAKALGVQTRPVILGPVSYLYLGKADKDSLDLEPISLLPKILPVYKELLQKLKEAGAEQVQIDEPVLVLDLPEAVQSKFKEAYDALVGADVPELILTTYFGDVRPNLKAIENLPVAGFHFDFVRVPEQLDEVASILKDGQTLSAGVVDGRNIWKTDFAKASAVVQKAIEKVGKDKVVVATSSSLLHTPVDLESETKLDAVIKDWFSFATQKLDEVVVIAKNVSGEDVSKQLEANAASIKARSESSITNDPKVQERLTTINEALATRKAAFPERLTEQKAKYNLPLFPTTTIGSFPIRINRNKFAKGQITAEEYEAFINKEIETVVRFQEEIGLDVLVHGEPERNDMVQYFGEQLNGFAFTTNGWVQSYGSRYVRPPIIVGDVSRPKAMTVKESVYAQSITSKPMKGMLTGPVTILRWSFPRDDVSGKIQALQLGLALRDEVNDLEGAGITVIQVDEPAIREGLPLRAGKERSDYLNWAAQSFRVATSGVENSTQIHSHFCYSDLDPNHIKALDADVVSIEFSPNYIQEFSEYPNHIGLGLFDIHSIPSKQEFVSRIEEILKVYPASKFWVNPDCGLKTRGWPEVKESLTNMVEAAKEFRAKYQ 802
                                    10        20        30        40        50        60        70        80        90       100 ||    121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675     ||689       699       711       721       731       741       751       761     ||
                                                                                                                               102|                                                                                                                                                                                                                                                                                                                                             450|                                                                                                                                                                                                                               681|                   708|                                                     767|
                                                                                                                                114                                                                                                                                                                                                                                                                                                                                              455                                                                                                                                                                                                                                686                    711                                                      802
   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 4L6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L6O)

(-) Gene Ontology  (14, 14)

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
    GLN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4l6o)
 

(-) 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
  4l6o
    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
  METE_CANAL | P82610
    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)
  2.1.1.14
    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
  METE_CANAL | P82610
    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
        METE_CANAL | P82610: 3ppc 3ppf 3ppg 3pph 4l5z 4l61 4l64 4l65 4l6h 4qqu

(-) Related Entries Specified in the PDB File

4l5z CRYSTAL STRUCTURE OF THE CANDIDA ALBICANS METHIONINE SYNTHASE IN COMPLEX WITH HOMOCYSTEINE
4l61 CRYSTAL STRUCTURE OF THE CANDIDA ALBICANS METHIONINE SYNTHASE IN COMPLEX WITH METHIONINE
4l64 CRYSTAL STRUCTURE OF THE CANDIDA ALBICANS METHIONINE SYNTHASE IN COMPLEX WITH 5-METHYL-TETRAHYDROFOLATE
4l65 CRYSTAL STRUCTURE OF THE CANDIDA ALBICANS METHIONINE SYNTHASE IN COMPLEX WITH 5-METHYL-TETRAHYDROFOLATE AND METHIONINE
4l6h CRYSTAL STRUCTURE OF THE CANDIDA ALBICANS METHIONINE SYNTHASE IN COMPLEX WITH METHOTREXATE AND HOMOCYSTEINE