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 :  HYDE FROM T. MARITIMA IN COMPLEX WITH S-ADENOSYL-L-CYSTEINE AND METHIONINE
 
Authors :  R. Rohac, P. Amara, A. Benjdia, L. Martin, P. Ruffie, A. Favier, O. Berte J. M. Mouesca, J. C. Fontecilla-Camps, Y. Nicolet
Date :  17 Dec 15  (Deposition) - 06 Apr 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A
Keywords :  Radical Sam Enzyme, Complex, Fefe-Hydrogenase Maturase, Thiazolidine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Rohac, P. Amara, A. Benjdia, L. Martin, P. Ruffie, A. Favier, O. Berteau, J. M. Mouesca, J. C. Fontecilla-Camps, Y. Nicolet
Carbon-Sulfur Bond-Forming Reaction Catalysed By The Radica Sam Enzyme Hyde.
Nat. Chem. V. 8 491 2016
PubMed-ID: 27102684  |  Reference-DOI: 10.1038/NCHEM.2490

(-) Compounds

Molecule 1 - [FEFE] HYDROGENASE MATURASE SUBUNIT HYDE
    Chains: A
    EC Number: 1.8.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TM_1269, THEMA_07990, TMARI_1274
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
15X81Ligand/IonS-ADENOSYL-L-CYSTEINE
2CL2Ligand/IonCHLORIDE ION
3CPS5Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
4MET1Mod. Amino AcidMETHIONINE
5SFS1Ligand/IonFE4-SE4 CLUSTER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , CYS A:67 , TYR A:69 , CYS A:70 , MET A:408binding site for residue SFS A 401
02AC2SOFTWAREGLN A:98 , PHE A:99 , GLY A:277 , GLU A:280 , ARG A:284 , MET A:324 , LEU A:330 , CPS A:404 , CPS A:405 , HOH A:514 , HOH A:559 , HOH A:566 , HOH A:608 , HOH A:694 , HOH A:709 , HOH A:724binding site for residue CPS A 402
03AC3SOFTWARELYS A:37 , ASP A:40 , LYS A:170 , ARG A:284 , SER A:297 , LYS A:315 , ASP A:316 , THR A:317 , HOH A:621 , HOH A:627 , HOH A:632 , HOH A:712 , HOH A:741binding site for residue CPS A 403
04AC4SOFTWAREARG A:29 , LYS A:315 , THR A:317 , ALA A:318 , CPS A:402 , CPS A:410 , HOH A:526 , HOH A:563 , HOH A:699 , HOH A:735 , HOH A:749binding site for residue CPS A 404
05AC5SOFTWARELYS A:128 , PRO A:321 , MET A:324 , LYS A:325 , GLU A:328 , CPS A:402 , HOH A:512 , HOH A:557 , HOH A:633 , HOH A:652 , HOH A:682 , HOH A:718 , HOH A:756 , HOH A:825binding site for residue CPS A 405
06AC6SOFTWAREARG A:54 , THR A:134 , ARG A:155binding site for residue CL A 406
07AC7SOFTWAREARG A:159 , MET A:291 , 5X8 A:409 , HOH A:847binding site for residue CL A 407
08AC8SOFTWAREGLN A:107 , SER A:108 , SER A:136 , GLY A:138 , ARG A:180 , TYR A:303 , SFS A:401 , 5X8 A:409 , HOH A:569 , HOH A:579 , HOH A:619 , HOH A:624binding site for residue MET A 408
09AC9SOFTWARETYR A:69 , GLN A:107 , ARG A:159 , GLU A:161 , MET A:199 , PRO A:229 , ILE A:231 , THR A:268 , THR A:269 , ALA A:270 , LEU A:305 , TYR A:306 , CL A:407 , MET A:408 , HOH A:534 , HOH A:619 , HOH A:622 , HOH A:768 , HOH A:770binding site for residue 5X8 A 409
10AD1SOFTWAREARG A:29 , GLU A:33 , GLU A:150 , THR A:247 , CPS A:404 , HOH A:668 , HOH A:743 , HOH A:771binding site for residue CPS A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FF0)

(-) Cis Peptide Bonds  (2, 3)

Asymmetric/Biological Unit
No.Residues
1Met A:115 -Pro A:116
2Ser A:297 -Pro A:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FF0)

(-) Exons   (0, 0)

(no "Exon" information available for 5FF0)

(-) 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 hhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee........................hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eee......hhhhhhhhh...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh....ee........hhhhh..............hhhhhhhhhhhhh..ee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ff0 A   2 TGREILEKLERREFTREVLKEALSINDRGFNEALFKLADEIRRKYVGDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYYMPDVISDIVKEIKKMGVAVTLSLGEWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPFIPHPDTPLANEKKGDFTLTLKMVALTRILLPDSNIPATTAMGTIVPGGREITLRCGANVIMPNWTPSPYRQLYQLYPGKISVFEKDTASIPSVMKMIELLGRKPGRDWGGRKRVFETM 408
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341     ||
                                                                                                                                                                                                                                                                                                                                                                                   347|
                                                                                                                                                                                                                                                                                                                                                                                    408
   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 5FF0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FF0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FF0)

(-) Gene Ontology  (9, 9)

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
    5X8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CPS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MET  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SFS  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:115 - Pro A:116   [ RasMol ]  
    Ser A:297 - Pro A:298   [ 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
  5ff0
    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
  HYDE_THEMA | Q9X0Z6
    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)
  1.8.-.-
    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
  HYDE_THEMA | Q9X0Z6
    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
        HYDE_THEMA | Q9X0Z6: 3ciw 3cix 3iix 3iiz 4jxc 4jy8 4jy9 4jyd 4jye 4jyf 5fep 5fes 5few 5fex 5fez 5ff2 5ff3 5ff4

(-) Related Entries Specified in the PDB File

3iix 3iiz 5fep 5fes 5few 5fex 5fez