Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BORDETELLA BRONCHISEPTICA ENZYME WBMF IN COMPLEX WITH NAD+ AND UDP
 
Authors :  N. J. Harmer, J. D. King, C. M. Palmer, D. Maskell, T. L. Blundell
Date :  25 May 07  (Deposition) - 02 Oct 07  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Protein-Nad+ Complex, Protein-Udp Complex, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. King, N. J. Harmer, A. Preston, C. M. Palmer, M. Rejzek, R. A. Field T. L. Blundell, D. J. Maskell
Predicting Protein Function From Structure--The Roles Of Short-Chain Dehydrogenase/Reductase Enzymes In Bordetella O-Antigen Biosynthesis.
J. Mol. Biol. V. 374 749 2007
PubMed-ID: 17950751  |  Reference-DOI: 10.1016/J.JMB.2007.09.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE NUCLEOTIDE SUGAR EPIMERASE/ DEHYDRATASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BBLPS1.16, WBMF
    Organism Scientific: BORDETELLA BRONCHISEPTICA
    Organism Taxid: 518

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , GLY A:22 , PHE A:23 , VAL A:24 , ASP A:44 , ASN A:45 , LEU A:46 , LEU A:47 , SER A:48 , ALA A:49 , SER A:66 , ILE A:67 , LEU A:86 , ALA A:87 , THR A:88 , HIS A:90 , ASN A:105 , THR A:109 , SER A:129 , ALA A:131 , TYR A:161 , LYS A:165 , PHE A:188 , GLN A:189 , ASN A:190 , VAL A:191 , ARG A:212 , HOH A:404 , HOH A:426 , HOH A:427 , HOH A:446 , HOH A:452BINDING SITE FOR RESIDUE NAD A 358
2AC2SOFTWAREASN A:190 , VAL A:214 , PHE A:218 , PRO A:229 , GLU A:231 , ALA A:236 , ARG A:238 , ILE A:273 , HOH A:495 , HOH A:496 , HOH A:600BINDING SITE FOR RESIDUE UDP A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q1T)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His A:90 -Gly A:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q1T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q1T)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q1T)

(-) Sequences/Alignments

Asymmetric 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:332
 aligned with O87989_BORBO | O87989 from UniProtKB/TrEMBL  Length:357

    Alignment length:350
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
         O87989_BORBO     6 NASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAGCSIAEKTFDDAKATEETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh...eeeee......hhhhh.....eeee.....hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...--------------............hhhhhhhhhhhhhhhhhhhhhh..eeeee...ee.............hhhhh..hhhhhhhhhhhh.....hhhhhh.ee..eehhhhhhhhhhhhhhh...eeee......eehhhhhhhhhhhhh...............----...hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1t A   6 NASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAG--------------EETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDN----FGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
                                    15        25        35        45        55        65        75        85        95       105       115       125      |  -         - |     155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    |  305       315       325       335       345       355
                                                                                                                                                        132            147                                                                                                                                                      300  305
   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 2Q1T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q1T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q1T)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (O87989_BORBO | O87989)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.

 Visualization

(-) Interactive Views

Asymmetric 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
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:90 - Gly A:91   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2q1t
    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
  O87989_BORBO | O87989
    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
  O87989_BORBO | O87989
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O87989_BORBO | O87989: 2pzj 2q1s 2q1u

(-) Related Entries Specified in the PDB File

2pzj SAME PROTEIN WITHOUT UDP SOAK
2q1s SAME PROTEIN WITHOUT UDP SOAK, COMPLEXED WITH NADH.