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 :  CYCLOALTERNAN-FORMING ENZYME FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH PENTASACCHARIDE SUBSTRATE
 
Authors :  S. H. Light, W. F. Anderson, Center For Structural Genomics Of Inf Diseases (Csgid)
Date :  08 Dec 15  (Deposition) - 21 Sep 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Complex, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Light, L. A. Cahoon, A. S. Halavaty, N. E. Freitag, W. F. Anderson
Structure To Function Of An Alpha-Glucan Metabolic Pathway That Promotes Listeria Monocytogenes Pathogenesis.
Nat Microbiol V. 2 16202 2016
PubMed-ID: 27819654  |  Reference-DOI: 10.1038/NMICROBIOL.2016.202

(-) Compounds

Molecule 1 - CYCLOALTERNAN-FORMING ENZYME
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Gene: LMO2446
    Mutation: YES
    Organism Scientific: LISTERIA MONOCYTOGENES SEROVAR 1/2A (STRAIN ATCC BAA-679 / EGD-E)
    Organism Taxid: 169963
    Strain: ATCC BAA-679 / EGD-E
    Synonym: LMO2446 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1GLC13Ligand/IonALPHA-D-GLUCOSE
2MG5Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:970 , GLU A:972 , THR A:989 , GLY A:992 , ASP A:1085binding site for residue MG A 1101
02AC2SOFTWAREASN A:377 , HOH A:1250 , HOH A:1255 , HOH A:1257 , HOH A:1314 , HOH A:2317binding site for residue MG A 1102
03AC3SOFTWAREASN A:833 , ASP A:847 , SER A:850 , HOH A:1640 , HOH A:2059 , HOH A:2161binding site for residue MG A 1103
04AC4SOFTWAREGLU A:401 , ASP A:403 , ASP A:407 , HOH A:1863 , HOH A:2010 , HOH A:2190binding site for residue MG A 1104
05AC5SOFTWARETYR A:851 , ASP A:852 , HOH A:2139 , HOH A:2155 , HOH A:2310binding site for residue MG A 1105
06AC6SOFTWAREASP A:798 , ASN A:801 , HIS A:805 , TYR A:813 , TYR A:814 , GLU A:972 , PHE A:973 , HIS A:975 , LEU A:976 , THR A:991 , HOH A:1216 , HOH A:1227 , HOH A:1230 , HOH A:1269 , HOH A:1271 , HOH A:1317 , HOH A:1326 , HOH A:1371 , HOH A:1506 , HOH A:1664binding site for Poly-Saccharide residues GLC A 1106 through GLC A 1109
07AC7SOFTWARETHR A:443 , TYR A:444 , TYR A:496 , GLU A:497 , GLN A:498 , ASN A:801 , TYR A:814 , GLU A:972 , PHE A:973 , HIS A:975 , LEU A:976 , THR A:991 , GLC A:1106 , HOH A:1216 , HOH A:1227 , HOH A:1269 , HOH A:1317 , HOH A:1432 , HOH A:1506 , HOH A:1664 , HOH A:1856 , HOH A:2046 , HOH A:2192binding site for Poly-Saccharide residues GLC A 1110 through GLC A 1111
08AC8SOFTWAREHIS A:985 , GLY A:996 , ASP A:998 , VAL A:1027 , GLU A:1028 , TRP A:1051 , ALA A:1080 , GLY A:1081 , ASN A:1083 , HOH A:1285 , HOH A:1329 , HOH A:1373binding site for Poly-Saccharide residues GLC A 1112 through GLC A 1113
09AC9SOFTWARETRP A:71 , ASN A:103 , ASN A:104 , HOH A:1276 , HOH A:1641 , HOH A:1669 , HOH A:2145binding site for Poly-Saccharide residues GLC A 1114 through GLC A 1115
10AD1SOFTWAREASN A:301 , TYR A:303 , ASN A:400 , GLU A:428 , GLN A:429 , GLU A:433 , TYR A:436 , TRP A:484 , TRP A:528 , LYS A:563 , ASN A:565 , ARG A:614 , TRP A:627 , ASP A:630 , PHE A:663 , HIS A:689 , GLU A:691 , HOH A:1237 , HOH A:1365 , HOH A:1517 , HOH A:1646binding site for Poly-Saccharide residues GLC A 1116 through GLC A 1118

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F7U)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:54 -Pro A:55
2Trp A:71 -Pro A:72
3Gly A:137 -Pro A:138
4Ser A:229 -Pro A:230
5Ser A:696 -Pro A:697

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F7U)

(-) Exons   (0, 0)

(no "Exon" information available for 5F7U)

(-) 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:1059
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee................ee.........eeeeeeee.....eeeeeeeee..ee...ee.eeeeee..eeeeeeeee......eeeeeeeeee.....eeeeeeeee..eeeeeeeeeeeee....eeeeeee.......eeeeeeee..eeeeeee..............eeee...eeeee...eeeeee....eeeeee....eeeee.......eeee.....eeeeeeeee......eeeee...........eeee.......hhhhhh....eeeeeee...eeeee.....eeeee......eeeeeeeeee.....eeeeee...hhhhhhhhhhhhhh.....hhhhh.eee......hhhhhhhhhhhhhhh.....eeee..........................hhhhh.......hhhhhhhhhhhh..eeeeee..ee......hhhhhhhhhhhhhh.......................ee....hhhhhhhhhhhhhhhhhh.....eee.................hhhhhhhhhhhhhhhhhhhhhhhhh.....ee.....hhhhh.eee......hhhhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh..eeee.............hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhh............eee...eee.........eeeeee...eeee.....eee..eeeeee.......eeee...eeeeee..................eeeeee....eeeeeeee.....eeeeeeeeeehhh.eeeeee......eeeeee.....eeee..ee.....hhhhhhhh..eeeee....eeeeee......eeeeee......ee.hhheee...ee..........eeee......eeeeeee.....eeeeeeeeee.....eeeeeee..eeeeeee.........eeeeeeeee...eeeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5f7u A   33 DGEYHSPYGDDDLYTVQPTERSPRDPKAGEDVILNITTWPIENGQDVWVEWTKNGVAQENVTAAYDYNSGNNTYWKADLGKFEKGDEITYTTKGSTNGGTAYESGPFTFYVTDWEYVQDVTSVVDNGDSITLNMTATAGDFSPKLYLSFEDLDTLRMELSPTGKETGHAGKSGYTVEDTAEKVTVTTEDLSIEIQKSPYRMEVHQADGTLLTSEYTTANSLGWLTDGKNVINQYQNNFMTPSDEAFYGFGERYDTINQRGKDVETYVYNEYQDQAQTERTYLAVPFFVSANKYGMYVNSDFHSQFQMASKVEDKYSFVLDNDGDMTNMLDYYVISGKDQNDIVNNYTDITGKTTLLPKWAFGLWMSANEWDRESDVSSALSNAKANDIPATGFVLEQWSDEETYYIWNNATYTAKKNGEAFSYDDFTFNGKWTDPKGMVDSVHDAGMNIVLWQVPVLKDDGTVYEQRDNDEEYMISQGYSADDGTGAPYRVPASQWFGNGILLDFTNKDAVDWWTSQREYLLTEVGIDGFKTNGGEMVWGRDTTFSNGEKGQEMRNRYPTDYVSSYFDFAKSINPEAVSFSRSGTSGAQKSGIYWSGDQTSTFDSFQASLKAGLSASTSGVSYWAWDMAGFTGDYPTAELYKRATAMAAFAPIMQFHSEKSDPSPSEERSPWNAVARTGDETILPTFQKYLYTRMNLLPYIYTAAKDTADNGKSMMRQMAMDYPEDVNARDLDEQYMFGDDLLVAPIVQEGQTEKEVYLPEGEWVDIWNGGVHPGGETISYYADVDTLPVFAKAGAIIPMNMTDGYQLGQNVGNDLKSYDNLTFRVYPSGDSEYSFYDDVNGGEMRDISVSEDFANEKVSVDLPAMADETTMQVFSTEPTSVTIDGADVAKADTLDAFNEATTGYYYDTVQNLTYVKAAAKDAKQAIVLNGVNHAPYEAEFGHLTNVTTASDHAGYTGTGFVAGFDAEKEAVEFDIDAVDGASDYTMEVRYSAGVEDATRTVYINGKKQQITLPKTANWDTWNTVEVPVTLQAGNNQVVFDFEADDTAGINFDHVVIKK 1091
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082
   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 5F7U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F7U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F7U)

(-) Gene Ontology  (8, 8)

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
    GLC  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:137 - Pro A:138   [ RasMol ]  
    Ser A:229 - Pro A:230   [ RasMol ]  
    Ser A:54 - Pro A:55   [ RasMol ]  
    Ser A:696 - Pro A:697   [ RasMol ]  
    Trp A:71 - Pro A:72   [ 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
  5f7u
    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
  Q8Y4J2_LISMO | Q8Y4J2
    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
  Q8Y4J2_LISMO | Q8Y4J2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8Y4J2_LISMO | Q8Y4J2: 4kmq 4kwu 5hpo 5hxm 5i0d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5F7U)