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 :  MOUSE POFUT1 IN COMPLEX WITH EGF(+) AND GDP
 
Authors :  Z. Li, J. M. Rini
Date :  21 Jul 16  (Deposition) - 17 May 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Li, K. Han, J. E. Pak, M. Satkunarajah, D. Zhou, J. M. Rini
Recognition Of Egf-Like Domains By The Notch-Modifying O-Fucosyltransferase Pofut1.
Nat. Chem. Biol. V. 13 757 2017
PubMed-ID: 28530709  |  Reference-DOI: 10.1038/NCHEMBIO.2381

(-) Compounds

Molecule 1 - GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
    Chains: A
    EC Number: 2.4.1.221
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PB-T-PAF
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: POFUT1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PEPTIDE-O-FUCOSYLTRANSFERASE 1,O-FUCT-1
 
Molecule 2 - EGF(+)
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: F7, CF7
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 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
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , PHE A:49 , GLY A:50 , ASN A:51 , HIS A:243 , ARG A:245 , TRP A:250 , ALA A:314 , THR A:315 , ASP A:316 , PRO A:339 , ALA A:342 , ASP A:345 , SER A:361 , SER A:362 , PHE A:363 , HOH A:517 , HOH A:525 , HOH A:610 , HOH A:659 , HOH A:777 , HOH A:780 , HOH B:102binding site for residue GDP A 403
2AC2SOFTWAREPHE A:170 , THR A:171 , GLN A:182 , ARG A:186 , HOH A:513 , HOH A:805binding site for residue GOL A 404
3AC3SOFTWAREASP A:35 , ALA A:37 , ASN A:67 , ARG A:106 , GLN A:351 , ARG A:376 , HOH A:520 , HOH A:536 , HOH A:541 , HOH A:595 , HOH A:637 , HOH A:668binding site for Mono-Saccharide NAG A 401 bound to ASN A 67
4AC4SOFTWAREASN A:165 , HOH A:564 , HOH A:757binding site for Mono-Saccharide NAG A 402 bound to ASN A 165

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:43 -A:45
2A:131 -A:145
3A:254 -A:288
4A:272 -A:359
5B:5 -B:16
6B:10 -B:25
7B:27 -B:36

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:83 -Pro A:84
2Asn A:151 -Pro A:152
3Phe A:204 -Pro A:205
4Arg A:237 -Pro A:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KY5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KY5)

(-) Exons   (0, 0)

(no "Exon" information available for 5KY5)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....hhhhhhhhhhhhhhhhhhhh.eeee..eee..........eeehhhhhh.hhhhhhh..eeehhhhhhhhhhhhhhhhh.eeeeehhhhhhh............hhhhhhhh......eeeee.....hhhhhhhhhhhh......eeee.........hhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.........hhhhhh.........hhhhhh.hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh......eee.....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhh...eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ky5 A  33 SWDLAGYLLYCPCMGRFGNQADHFLGSLAFAKLLNRTLAVPPWIEYQHHKPPFTNLHVSYQKYFKLEPLQAYHRVVSLEDFMENLAPSHWPPEKRVAYCFEVAAQRSPDKKTCPMKEGNPFGPFWDQFHVSFNKSELFTGISFSASYKEQWTQRFPAKEHPVLALPGAPAQFPVLEEHRELQKYMVWSDEMVRTGEALISAHLVRPYVGIHLRIGSDWKNACAMLKDGTAGSHFMASPQCVGYSRSTATPLTMTMCLPDLKEIQRAVTLWVRALNARSVYIATDSESYVSEIQQLFKDKVRVVSLKPEVAQIDLYILGQADHFIGNCVSSFTAFVKRERDLHGRQSSFFGMD 384
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382  


Chain B from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh......eeee....eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 5ky5 B   1 DIDECASNPCQNGGTCVNTVGSYTCLCPPGFTGPNCEDDI  40
                                    10        20        30        40
   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 5KY5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KY5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KY5)

(-) Gene Ontology  (16, 16)

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
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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
    Arg A:237 - Pro A:238   [ RasMol ]  
    Asn A:151 - Pro A:152   [ RasMol ]  
    Phe A:204 - Pro A:205   [ RasMol ]  
    Pro A:83 - Pro A:84   [ 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
  5ky5
    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
  OFUT1_MOUSE | Q91ZW2
    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)
  2.4.1.221
    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
  OFUT1_MOUSE | Q91ZW2
    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
        OFUT1_MOUSE | Q91ZW2: 5kxh 5kxq 5ky0 5ky2 5ky3 5ky4 5ky7 5ky8 5ky9

(-) Related Entries Specified in the PDB File

5kxh 5kxq 5ky0 5ky2 5ky3 5ky4 5ky7 5ky8 5ky9