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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI FLAVIN TRAFFICKING PROTEIN, AN FMN TRANSFERASE, E169K MUTANT
 
Authors :  D. R. Tomchick, C. A. Brautigam, R. K. Deka, M. V. Norgard
Date :  02 Jan 15  (Deposition) - 16 Dec 15  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Flavin Transferase, Bimetal Center, Lipoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Deka, C. A. Brautigam, W. Z. Liu, D. R. Tomchick, M. V. Norgard
Molecular Insights Into The Enzymatic Diversity Of Flavin-Trafficking Protein (Ftp; Formerly Apbe) In Flavoprotein Biogenesis In The Bacterial Periplasm.
Microbiologyopen V. 5 21 2016
PubMed-ID: 26626129  |  Reference-DOI: 10.1002/MBO3.306

(-) Compounds

Molecule 1
    Chains: A, B, C, D
    EC Number: 2.7.1.180
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21 NESG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SOLUBLE FRAGMENT, UNP RESIDUES 21-351
    Gene: APBE, YOJK, YOJL, B2214, JW5368
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: FLAVIN TRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:166 , ASP A:280 , ASP A:283 , THR A:284 , HOH A:743binding site for residue CA A 501
02AC2SOFTWARELYS A:134 , THR A:137 , HOH A:618 , HOH A:669 , HOH A:693 , HOH A:698binding site for residue NA A 502
03AC3SOFTWARETHR B:166 , ASP B:280 , ASP B:283 , THR B:284 , HOH B:669binding site for residue CA B 501
04AC4SOFTWARETHR C:166 , ASP C:280 , ASP C:283 , THR C:284 , HOH C:683 , HOH C:730binding site for residue CA C 501
05AC5SOFTWARELYS C:134 , THR C:137 , HOH C:651 , HOH C:703binding site for residue NA C 502
06AC6SOFTWARELEU C:289 , GLY C:290 , PRO C:291 , GLU C:292 , LYS C:293binding site for residue EDO C 503
07AC7SOFTWAREGLN C:120binding site for residue EDO C 504
08AC8SOFTWARETHR D:166 , ASP D:280 , ASP D:283 , THR D:284 , HOH D:759binding site for residue CA D 501
09AC9SOFTWARELYS D:134 , THR D:137 , HOH D:699 , HOH D:715 , HOH D:754binding site for residue NA D 502
10AD1SOFTWARESER A:76 , PRO A:77 , PRO D:77 , TRP D:78 , PRO D:79 , EDO D:504 , HOH D:601 , HOH D:723binding site for residue EDO D 503
11AD2SOFTWAREPRO A:77 , TYR A:152 , TRP D:78 , EDO D:503 , HOH D:679binding site for residue EDO D 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XGW)

(-) 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhhhhhhhhhhh.eeeee....eeeee...........hhhhhhhhhhhhhhhhh....eeeee..eeeee..........eee..eee.....eeeeee..........................eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgw A  12 ATEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFGPEQVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGKGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQQAVVDINGHGISTSGSYRNYYEGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLV 328
                                    21        31        41        51        61        71        81        91       101       111       123       133       143       153       163       173       183       193       203       213|      232       242 ||    254       264       274       284       294       304       314       324    
                                                                                                                                     119|                                                                                        213|                  244|                                                                                 
                                                                                                                                      122                                                                                         223                   247                                                                                 


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhh..ee.....eee..hhhhhhhhhhhhhhh.eeeee....eeeee...........hhhhhhhhhhhhhhhhh....eeeee..eeeee..........ee.....ee....eeeeee.hhhhheee..eee...............eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgw B  13 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFGPEQQPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGKGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKPAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLV 328
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  ||   230       240       250       260       270       280       290       300       310       320        
                                                                                                                                                                                                                                    215|                                                                                                        
                                                                                                                                                                                                                                     224                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhhh.eeeee....eeeee...........hhhhhhhhhhhhhhhhh....eeeee..eeeee..........ee.......ee....eeeeee.......ee..ee................eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgw C  13 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFQPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGKGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKPTQAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVS 329
                                    22        32        42        52        62        72        82        92       102       112  ||   126       136       146       156       166       176       186       196       206       216|      232       242       252       262       272       282       292       302       312       322       
                                                                                                                                115|                                                                                             216|                                                                                                          
                                                                                                                                 120                                                                                              223                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhhhhh...........hhhhhhhhhhhhhhh.eeeee....eeeee...........hhhhhhhhhhhhhhhhh....eeeee..eeeee..........ee.....ee.....eeeeee..........ee....ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgw D  13 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFGPEQQPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGKGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKPAVVDINGHGISTSGSYRNKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVS 329
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  ||   230       240||     256       266       276       286       296       306       316       326   
                                                                                                                                                                                                                                    215|              241|                                                                                 
                                                                                                                                                                                                                                     224               248
   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 4XGW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xgw)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4xgw
    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
  APBE_ECOLI | P0AB85
    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)
  2.7.1.180
    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
  APBE_ECOLI | P0AB85
    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
        APBE_ECOLI | P0AB85: 2o18 4xgv 4xgx

(-) Related Entries Specified in the PDB File

4xgv 4XGV CONTAINS THE WILD-TYPE PROTEIN.