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 SE-ADENOSYL-L-SELENOCYSTEINE (TFINAL OF THE REACTION)
 
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 :  1.32
Chains :  Asym./Biol. Unit :  A
Keywords :  Radical Sam Enzyme, Complex, Fefe-Hydrogenase Maturase, Thazolidine, 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  (7, 13)

Asymmetric/Biological Unit (7, 13)
No.NameCountTypeFull Name
15AD1Ligand/Ion5'-DEOXYADENOSINE
2CL3Ligand/IonCHLORIDE ION
3CPS5Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
4MET1Mod. Amino AcidMETHIONINE
5OTY1Mod. Amino Acid2-HYDROXY-L-TYROSINE
6SEC1Ligand/IonSELENOCYSTEINE
7SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , CYS A:67 , CYS A:70 , MET A:411binding site for residue SF4 A 401
02AC2SOFTWAREGLN A:98 , PHE A:99 , GLY A:100 , GLY A:277 , GLU A:280 , ARG A:284 , MET A:324 , LEU A:330 , CPS A:406 , HOH A:535 , HOH A:605 , HOH A:612 , HOH A:673 , HOH A:686 , HOH A:764 , HOH A:941binding 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:595 , HOH A:599 , HOH A:628 , HOH A:684 , HOH A:746 , HOH A:892binding site for residue CPS A 403
04AC4SOFTWAREARG A:29 , GLU A:33 , THR A:247 , LEU A:250 , CPS A:405 , HOH A:516 , HOH A:632 , HOH A:701 , HOH A:957binding site for residue CPS A 404
05AC5SOFTWAREARG A:29 , GLU A:314 , LYS A:315 , THR A:317 , ALA A:318 , CPS A:404 , CPS A:406 , HOH A:586 , HOH A:621 , HOH A:656 , HOH A:661 , HOH A:689binding site for residue CPS A 405
06AC6SOFTWARELYS A:128 , PRO A:321 , MET A:324 , LYS A:325 , GLU A:328 , CPS A:402 , CPS A:405 , HOH A:662 , HOH A:781 , HOH A:784 , HOH A:797 , HOH A:894 , HOH A:937 , HOH A:954binding site for residue CPS A 406
07AC7SOFTWAREARG A:54 , THR A:134 , ARG A:155binding site for residue CL A 407
08AC8SOFTWAREARG A:159 , SEC A:412 , HOH A:818binding site for residue CL A 408
09AC9SOFTWARETYR A:306 , SEC A:412binding site for residue CL A 409
10AD1SOFTWARETYR A:69 , ARG A:159 , GLU A:161 , MET A:199 , PRO A:229 , ILE A:231 , LEU A:305 , TYR A:306 , MET A:411 , SEC A:412 , HOH A:649 , HOH A:698binding site for residue 5AD A 410
11AD2SOFTWARESER A:108 , SER A:136 , GLY A:138 , ARG A:180 , TYR A:303 , LEU A:305 , SF4 A:401 , 5AD A:410 , HOH A:569 , HOH A:601 , HOH A:649binding site for residue MET A 411
12AD3SOFTWAREGLN A:107 , ARG A:159 , THR A:268 , THR A:269 , ALA A:270 , TYR A:306 , CL A:408 , CL A:409 , 5AD A:410 , HOH A:529 , HOH A:609 , HOH A:697 , HOH A:793binding site for residue SEC A 412

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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 5FEX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FEX)

(-) 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..eeee..ee.....hhhhhhhhhhhhhhhh..ee..ee...............hhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh....ee........hhhhh..............hhhhhhhhhhhhh..ee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fex A   2 TGREILEKLERREFTREVLKEALSINDRGFNEALFKLADEIRRKYVGDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYyMPDVISDIVKEIKKMGVAVTLSLGEWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPFIPHPDTPLANEKKGDFTLTLKMVALTRILLPDSNIPATTAMGTIVPGGREITLRCGANVIMPNWTPSPYRQLYQLYPGKISVFEKDTASIPSVMKMIELLGRKPGRDWGGRKRVFETM 411
                                    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     ||
                                                                                                                                          114-OTY                                                                                                                                                                                                                                  347|
                                                                                                                                                                                                                                                                                                                                                                                    411
   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 5FEX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    5AD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CPS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MET  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OTY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ 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 ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ 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
  5fex
    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 5fez 5ff0 5ff2 5ff3 5ff4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5FEX)