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 THE WBKC N-FORMYLTRANSFERASE FROM BRUCELLA MELITENSIS IN COMPLEX WITH GDP-PEROSAMINEA AND N-10-FORMYLTETRAHYDROFOLATE
 
Authors :  A. S. Riegert, D. P. Chantigian, J. B. Thoden, H. M. Holden
Date :  26 May 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Deoxysugar, Brucellosis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Riegert, D. P. Chantigian, J. B. Thoden, P. A. Tipton, H. M. Holden
Biochemical Characterization Of Wbkc, An N-Formyltransferas From Brucella Melitensis.
Biochemistry 2017
PubMed-ID: 28636341  |  Reference-DOI: 10.1021/ACS.BIOCHEM.7B00494

(-) Compounds

Molecule 1 - GDP-MANNOSE 4,6-DEHYDRATASE / GDP-4-AMINO-4,6-DIDEOXY-D- MANNOSE FORMYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.2.-, 4.2.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Gene: BMEI1418
    Mutation: YES
    Organism Scientific: BRUCELLA MELITENSIS BIOTYPE 1 (STRAIN 16M / ATCC 23456 / NCTC 10094)
    Organism Taxid: 224914
    Strain: 16M / ATCC 23456 / NCTC 10094

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
11YA2Ligand/IonN-{4-[{[(6S)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}(FORMYL)AMINO]BENZOYL}-L-GLUTAMIC ACID
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3JB21Ligand/IonGDP-PEROSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:87 , ARG A:88 , SER A:89 , LEU A:90 , ILE A:91 , ASN A:105 , HIS A:136 , MET A:138 , ASP A:139 , GLU A:140 , ASN A:141 , ALA A:142 , ASP A:143 , JB2 A:302 , HOH A:418 , HOH A:442 , HOH A:448 , ARG B:212binding site for residue 1YA A 301
2AC2SOFTWAREARG A:45 , ARG A:88 , GLY A:116 , THR A:117 , ASN A:118 , VAL A:120 , PHE A:165 , LEU A:203 , MET A:225 , PHE A:227 , PHE A:230 , PRO A:231 , 1YA A:301 , HOH A:406 , HOH A:412 , HOH A:443 , HOH A:445 , HOH A:446 , HOH A:478 , ARG B:212binding site for residue JB2 A 302
3AC3SOFTWAREARG B:88 , SER B:89 , LEU B:90 , ILE B:91 , ASN B:105 , HIS B:136 , MET B:138 , ASP B:139 , GLU B:140 , ASN B:141 , ALA B:142 , ASP B:143 , ARG B:201 , HOH B:416 , HOH B:441 , HOH B:468binding site for residue 1YA B 301
4AC4SOFTWAREARG B:88 , THR B:117 , ASN B:118 , LEU B:203 , MET B:225 , PHE B:227 , PHE B:230 , PRO B:231 , HOH B:406binding site for residue GDP B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:111 -Pro A:112
2Pro A:228 -Pro A:229
3Leu B:111 -Pro B:112
4Pro B:228 -Pro B:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VYU)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhh.eee.....hhhhhhhhhhhh..eeeee......hhhhhhh....eeeee.......ee.hhhhhhhhh...eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee...hhhhhh.....hhhhhhhhhhhh..............hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyu A   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENADTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLYYVPSIDIYR 251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   ||  247    
                                                                                                                                                                                                                                                                   235|         
                                                                                                                                                                                                                                                                    242         


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeee......hhhhhhh....eeeee.......ee.hhhhhhhhhh..eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee...hhhhhh.....hhhhhhhhhhhhh.......eee....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyu B   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENADTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIDGKVYYVP 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 5VYU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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
    1YA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    JB2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:111 - Pro A:112   [ RasMol ]  
    Leu B:111 - Pro B:112   [ RasMol ]  
    Pro A:228 - Pro A:229   [ RasMol ]  
    Pro B:228 - Pro B:229   [ 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
  5vyu
    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
  F8WJP6_BRUME | F8WJP6
    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)
  2.1.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  4.2.1.47
    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
  F8WJP6_BRUME | F8WJP6
    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
        F8WJP6_BRUME | F8WJP6: 5vyr 5vys 5vyt

(-) Related Entries Specified in the PDB File

5vyr 5vys 5vyt