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(-) Description

Title :  MOUSE POFUT1 IN COMPLEX WITH O-GLUCOSYLATED MOUSE FACTOR VII EGF1 AND GDP
 
Authors :  Z. Li, J. M. Rini
Date :  20 Jul 16  (Deposition) - 17 May 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
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 - COAGULATION FACTOR VII
    Chains: B
    EC Number: 3.4.21.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: F7, CF7
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SERUM PROTHROMBIN CONVERSION ACCELERATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3GOL3Ligand/IonGLYCEROL
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , PHE A:49 , GLY A:50 , ASN A:51 , HIS A:243 , ARG A:245 , 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:514 , HOH A:528 , HOH A:535 , HOH A:621 , HOH A:654 , HOH A:720 , HOH A:737 , HOH A:743binding site for residue GDP A 403
2AC2SOFTWAREPHE A:170 , THR A:171 , GLN A:182 , ARG A:186 , HOH A:740binding site for residue GOL A 404
3AC3SOFTWARELYS A:64 , ASN A:67 , HIS A:105 , HOH A:685binding site for residue GOL A 405
4AC4SOFTWARELEU A:65 , LEU A:66 , LYS A:180 , THR A:184 , HIS A:374 , ARG A:376 , NAG A:401 , HOH A:526 , HOH A:584binding site for residue GOL A 406
5AC5SOFTWAREASP A:35 , ALA A:37 , ASN A:67 , ARG A:106 , GLN A:351 , ALA A:352 , ARG A:376 , GOL A:406 , HOH A:509 , HOH A:524 , HOH A:540 , HOH A:549 , HOH A:588 , HOH A:681binding site for Mono-Saccharide NAG A 401 bound to ASN A 67
6AC6SOFTWAREASN A:165 , HOH A:645binding site for Mono-Saccharide NAG A 402 bound to ASN A 165
7AC7SOFTWAREARG A:138 , GLN B:90 , SER B:93 , TYR B:109 , HOH B:1101 , HOH B:1116binding site for Mono-Saccharide BGC B 1001 bound to SER B 93

(-) 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:91 -B:102
6B:96 -B:111
7B:113 -B:122

(-) Cis Peptide Bonds  (5, 5)

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
5Gly B:88 -Asp B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KY2)

(-) Exons   (0, 0)

(no "Exon" information available for 5KY2)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....hhhhhhhhhhhhhhhhhhhh.eeee..eee..........eeehhhhhh.hhhhhhh..eeehhhhhhhhhhhhhhhhh.eeeeehhhhhh.............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
                 5ky2 A  30 GAPSWDLAGYLLYCPCMGRFGNQADHFLGSLAFAKLLNRTLAVPPWIEYQHHKPPFTNLHVSYQKYFKLEPLQAYHRVVSLEDFMENLAPSHWPPEKRVAYCFEVAAQRSPDKKTCPMKEGNPFGPFWDQFHVSFNKSELFTGISFSASYKEQWTQRFPAKEHPVLALPGAPAQFPVLEEHRELQKYMVWSDEMVRTGEALISAHLVRPYVGIHLRIGSDWKNACAMLKDGTAGSHFMASPQCVGYSRSTATPLTMTMCLPDLKEIQRAVTLWVRALNARSVYIATDSESYVSEIQQLFKDKVRVVSLKPEVAQIDLYILGQADHFIGNCVSSFTAFVKRERDLHGRQSSFFGMD 384
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379     


Chain B from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh......eeeee..eeeee....ee.....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 5ky2 B  87 DGDQCASNPCQNGGTCQDHLKSYVCFCLLDFEGRNCEKSK 126
                                    96       106       116       126
   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 5KY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KY2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KY2)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:237 - Pro A:238   [ RasMol ]  
    Asn A:151 - Pro A:152   [ RasMol ]  
    Gly B:88 - Asp B:89   [ RasMol ]  
    Phe A:204 - Pro A:205   [ RasMol ]  
    Pro A:83 - Pro A:84   [ RasMol ]  
 

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  5ky2
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  OFUT1_MOUSE | Q91ZW2
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  2.4.1.221
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  3.4.21.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        FA7_MOUSE | P70375: 5kxh 5ky3
        OFUT1_MOUSE | Q91ZW2: 5kxh 5kxq 5ky0 5ky3 5ky4 5ky5 5ky7 5ky8 5ky9

(-) Related Entries Specified in the PDB File

5khx 5kx0 5kx3 5kx4 5kx7 5kx8 5kx9 5kxq