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 :  ACETYLTRANSFERASE DOMAIN OF PGLB FROM NEISSERIA GONORRHOEAE FA1090 IN COMPLEX WITH ACETYL COENZYME A
 
Authors :  M. J. Morrison, B. Imperiali
Date :  14 Aug 13  (Deposition) - 02 Oct 13  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Left-Handed Beta-Helix, Rossmann Fold, Acetyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Morrison, B. Imperiali
Biochemical Analysis And Structure Determination Of Bacterial Acetyltransferases Responsible For The Biosynthesis Of Udp-N, N'-Diacetylbacillosamine.
J. Biol. Chem. V. 288 32248 2013
PubMed-ID: 24064219  |  Reference-DOI: 10.1074/JBC.M113.510560

(-) Compounds

Molecule 1 - PILIN GLYCOSYLATION PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-30B(+)
    Expression System Strain: BL21(DE3)PLYSS RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 197-403
    Gene: NGO0085
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 242231
    Strain: FA 1090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACO3Ligand/IonACETYL COENZYME *A
2NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:332 , GLY A:351 , ARG A:368 , GLN A:369 , VAL A:386 , ASN A:398 , PRO A:399 , LYS A:401 , PRO B:345 , ARG B:360 , GLY B:362 , THR B:363 , GLY B:380 , ALA B:381 , ALA B:396 , HOH B:619BINDING SITE FOR RESIDUE ACO A 501
2AC2SOFTWAREHIS A:348 , HIS B:348 , HIS C:348BINDING SITE FOR RESIDUE NA A 502
3AC3SOFTWAREASP B:332 , HIS B:333 , SER B:350 , GLY B:351 , ARG B:368 , GLN B:369 , VAL B:386 , ASN B:398 , PRO B:399 , LYS B:401 , HOH B:616 , SER C:344 , ARG C:360 , GLY C:362 , THR C:363 , GLY C:380 , ALA C:381 , ALA C:396 , HOH C:620BINDING SITE FOR RESIDUE ACO B 501
4AC4SOFTWARESER A:344 , ARG A:360 , GLY A:362 , THR A:363 , GLY A:380 , ALA A:381 , ALA A:396 , GLY A:397 , LEU A:403 , ASP C:332 , SER C:350 , GLY C:351 , ARG C:368 , GLN C:369 , VAL C:386 , ASN C:398 , PRO C:399 , LYS C:401 , HOH C:624BINDING SITE FOR RESIDUE ACO C 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M99)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:398 -Pro A:399
2Asn B:398 -Pro B:399
3Asn C:398 -Pro C:399

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M99)

(-) Exons   (0, 0)

(no "Exon" information available for 4M99)

(-) 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:206
                                                                                                                                                                                                                                              
               SCOP domains d4m99a_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh...eeeee......ee..eeeee..hhhhhh.....eeeee...hhhhhhhhhhhhhhh......ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee........eee....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m99 A 198 GNRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRTQGSVNGFPVIGTTLLLENSLSPEQFDITVAVGNNRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL 403
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397      


Chain B from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains d4m99b_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh...eeeee.....eee..eeeeehhhhh.......eeeee...hhhhhhhhhhhhhhh......ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee........eee....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m99 B 198 GNRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRTQGSVNGFPVIGTTLLLNSLSPEQFDITVAVGNNRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL 403
                                   207       217       227       237       247  ||   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398     
                                                                              250|                                                                                                                                                       
                                                                               252                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains d4m99c_ C: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh...eeeee......ee..eeeee.hhhhhh......eeeee...hhhhhhhhhhhhhhh......ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee........eee....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m99 C 198 GNRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRTQGSVNGFPVIGTTLLLENSLSPEQFDITVAVGNNRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL 403
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M99)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M99)

(-) Gene Ontology  (3, 3)

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
    ACO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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
    Asn A:398 - Pro A:399   [ RasMol ]  
    Asn B:398 - Pro B:399   [ RasMol ]  
    Asn C:398 - Pro C:399   [ 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
  4m99
    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
  Q5FAE1_NEIG1 | Q5FAE1
    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
  Q5FAE1_NEIG1 | Q5FAE1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5FAE1_NEIG1 | Q5FAE1: 4m98

(-) Related Entries Specified in the PDB File

4m98 4m9c