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 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE (KDSC) FROM MORAXELLA CATARRHALIS IN COMPLEX WITH MAGNESIUM ION
 
Authors :  S. Dhindwal, S. Tomar, P. Kumar
Date :  15 May 14  (Deposition) - 11 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Had Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Dhindwal, P. Priyadarshini, D. N. Patil, S. Tapas, P. Kumar, S. Tomar, P. Kumar
Ligand-Bound Structures Of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Moraxella Catarrhalis Reveal A Water Channel Connecting To The Active Site For The Second Step Of Catalysis
Acta Crystallogr. , Sect. D V. 71 239 2015
PubMed-ID: 25664734  |  Reference-DOI: 10.1107/S1399004714025218

(-) Compounds

Molecule 1 - 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC
    Chains: A, B, C, D
    EC Number: 3.1.3.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28C
    Expression System Vector Type: PLASMID
    Organism Scientific: MORAXELLA CATARRHALIS BC8
    Organism Taxid: 857574

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:17 , ASP A:19 , ASP A:110 , HOH A:2031 , HOH A:2033 , HOH A:2034BINDING SITE FOR RESIDUE MG A 175
02AC2SOFTWAREASP B:17 , ASP B:19 , ASP B:110 , HOH B:2018 , HOH B:2019 , HOH B:2023BINDING SITE FOR RESIDUE MG B 175
03AC3SOFTWAREASP C:17 , ASP C:19 , ASP C:110 , HOH C:2014 , HOH C:2017 , HOH C:2018BINDING SITE FOR RESIDUE MG C 175
04AC4SOFTWAREASP D:17 , ASP D:19 , ASP D:110 , HOH D:2017 , HOH D:2019 , HOH D:2020BINDING SITE FOR RESIDUE MG D 175
05AC5SOFTWARETYR D:5 , LYS D:160 , HOH D:2153BINDING SITE FOR RESIDUE EDO D1000
06AC6SOFTWAREHOH A:2214 , GLU D:153 , GLU D:156 , LEU D:157 , LYS D:160 , HOH D:2009BINDING SITE FOR RESIDUE EDO D1001
07AC7SOFTWAREGLU A:153 , GLU A:156 , LYS A:160 , HOH A:2015BINDING SITE FOR RESIDUE EDO A1000
08AC8SOFTWAREASP B:166 , GLN B:173 , HOH B:2207BINDING SITE FOR RESIDUE EDO B1000
09AC9SOFTWAREGLU A:35 , LYS A:37 , ARG A:63 , SER A:64 , SER A:65 , VAL A:68 , GLN A:82 , HOH A:2037BINDING SITE FOR RESIDUE EDO A1001
10BC1SOFTWAREGLN C:84 , ASP C:86 , THR C:89 , HOH C:2089BINDING SITE FOR RESIDUE EDO C1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UM7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UM7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UM7)

(-) Exons   (0, 0)

(no "Exon" information available for 4UM7)

(-) 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:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeee..hhhhhhhhhhh.eeee....hhhhhhh..ee.......hhhhhhhhhhhhhh.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4um7 A  -1 GHMNEIYQKAKHIKLFAMDVDGILSDGQIIYNSEGTETKAFYVQDGLGLQALKQSGIILAIITGRSSAMVDRRAKELGISHIIQGQDDKLTALVGLTKKLGIELSHCAYIGDDLPDLKAVREAGFGISVPNGCEQTRAVSDYITTKTGGNGAVREVCELILKAQNNFDAFIATFQ 173
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168     


Chain B from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhh..hhh.eeee..hhhhhhhhhhh.eeee....hhhhhhh..ee.......hhhhhhhhhhhhhh.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4um7 B   1 MNEIYQKAKHIKLFAMDVDGILSDGQIIYNSEGTETKAFYVQDGLGLQALKQSGIILAIITGRSSAMVDRRAKELGISHIIQGQDDKLTALVGLTKKLGIELSHCAYIGDDLPDLKAVREAGFGISVPNGCEQTRAVSDYITTKTGGNGAVREVCELILKAQNNFDAFIATFQ 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain C from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh...eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeee..hhhhhhhhhhh.eeee....hhhhhhh..ee.......hhhhhhhhhhhhhh.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4um7 C   0 HMNEIYQKAKHIKLFAMDVDGILSDGQIIYNSEGTETKAFYVQDGLGLQALKQSGIILAIITGRSSAMVDRRAKELGISHIIQGQDDKLTALVGLTKKLGIELSHCAYIGDDLPDLKAVREAGFGISVPNGCEQTRAVSDYITTKTGGNGAVREVCELILKAQNNFDAFIATFQ 173
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169    


Chain D from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh...eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeee..hhhhhhhhhhh.eeee....hhhhhhh..ee.......hhhhhhhhhhhhhh.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4um7 D   0 HMNEIYQKAKHIKLFAMDVDGILSDGQIIYNSEGTETKAFYVQDGLGLQALKQSGIILAIITGRSSAMVDRRAKELGISHIIQGQDDKLTALVGLTKKLGIELSHCAYIGDDLPDLKAVREAGFGISVPNGCEQTRAVSDYITTKTGGNGAVREVCELILKAQNNFDAFIATFQ 173
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   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 4UM7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UM7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4UM7)

 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
    EDO  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4um7)
 

(-) 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
  4um7
    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
  A0A0J9X241_M | A0A0J9X241
    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)
  3.1.3.45
    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
  A0A0J9X241_M | A0A0J9X241
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0J9X241_M | A0A0J9X241: 4um5 4umd 4ume 4umf

(-) Related Entries Specified in the PDB File

4um5 CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH MAGNESIUM ION AND PHOSPHATE ION
4umd CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH CITRATE
4ume CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH MAGNESIUM ION AND KDO MOLECULE
4umf CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH MAGNESIUM ION, PHOSPHATE ION AND KDO MOLECULE