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(-) Description

Title :  CRYSTAL STRUCTURE OF DROSOPHILA POGLUT1 (RUMI) COMPLEXED WITH ITS SUBSTRATE PROTEIN (EGF REPEAT) AND UDP
 
Authors :  H. J. Yu, H. L. Li
Date :  09 Dec 15  (Deposition) - 20 Jul 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycosyltransferase, Protein O-Glucosyltransferase, Notch Regulation, Egf Repeat, Transferase-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Yu, H. L. Li
Crystal Structure Of Drosophila Poglut1 (Rumi) Complexed With Its Substrate Protein (Egf Repeat) And Udp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - O-GLUCOSYLTRANSFERASE RUMI
    Chains: A
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 21-407
    Gene: RUMI, CG31152
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - COAGULATION FACTOR IX
    Chains: B
    EC Number: 3.4.21.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 92-130
    Gene: F9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:200 , ARG A:229 , GLY A:230 , SER A:231 , THR A:233 , ARG A:237 , GLU A:275 , VAL A:276 , PHE A:278 , GLY A:292 , SER A:296 , ARG A:298 , GOL A:502 , HOH A:603 , HOH A:611 , HOH A:667 , HOH A:670 , HOH B:104binding site for residue UDP A 501
2AC2SOFTWAREARG A:125 , ASP A:151 , PRO A:191 , ALA A:295 , SER A:296 , PHE A:297 , UDP A:501 , HOH A:610 , SER B:53binding site for residue GOL A 502
3AC3SOFTWAREHIS A:196 , MET A:206 , LYS A:209 , SER A:277 , PHE A:278 , GLU A:279 , HOH A:667binding site for residue SO4 A 503
4AC4SOFTWAREARG A:229 , VAL A:276binding site for residue SO4 A 504
5AC5SOFTWAREARG A:372 , MET A:373 , LYS A:374 , HOH A:673binding site for residue SO4 A 505
6AC6SOFTWARELYS A:49 , GLY A:313 , ASP A:314 , LYS A:334 , SER A:335 , HOH A:651binding site for residue SO4 A 506
7AC7SOFTWARESER A:239 , SER A:338 , GLN A:339 , HOH A:614binding site for residue SO4 A 507

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:64 -A:75
2A:73 -A:378
3A:120 -A:126
4A:282 -A:305
5B:51 -B:62
6B:56 -B:71
7B:73 -B:82

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:160 -Asn A:161
2Gly A:165 -Pro A:166
3Gly A:405 -Pro A:406

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F85)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F85)

(-) Exons   (0, 0)

(no "Exon" information available for 5F85)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh....hhhhhhhhhhhheeeee....eee.....hhhhhhhhhhhhhhhhhhh..eeeee....................ee.........ee..hhhhh..............hhhhhhhhhhhhhhhhhhhhheeeeeeeee..hhhhhhhhhhhhhh...eeeeee......hhhhhh........hhhhhh.eeeeeee......hhhhhhhh...eeeee..................eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f85 A  42 NEDEFSFKIRRQIEKANADYKPCSSDPQDSDCSCHANVLKRDLAPYKSTGVTRQMIESSARYGTKYKIYGHRLYRDANCMFPARCEGIEHFLLPLVATLPDMDLIINTRDYPQLNAAWGNAAGGPVFSFSKTKEYRDIMYPAWTFWAGGPATKLHPRGIGRWDQMREKLEKRAAAIPWSQKRSLGFFRGSRTSDERDSLILLSRRNPELVEAQYTKNQGWKSPKDTLDAPAADEVSFEDHCKYKYLFNFRGVAASFRLKHLFLCKSLVFHVGDEWQEFFYDQLKPWVHYVPLKSYPSQQEYEHILSFFKKNDALAQEIAQRGYDFIWEHLRMKDIKCYWRKLLKRYVKLLQYEVKPEDQLIYIGP 406
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     


Chain B from PDB  Type:PROTEIN  Length:39
                                                                       
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh......eeee....eeee....ee.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 5f85 B  48 GDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCELLE  86
                                    57        67        77
   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 5F85)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F85)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F85)

(-) Gene Ontology  (40, 41)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:160 - Asn A:161   [ RasMol ]  
    Gly A:165 - Pro A:166   [ RasMol ]  
    Gly A:405 - Pro A:406   [ RasMol ]  
 

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  5f85
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  RUMI_DROME | Q8T045
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 Related Entries

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

UniProtKB/Swiss-Prot
        FA9_HUMAN | P00740: 1cfh 1cfi 1edm 1ixa 1mgx 1nl0 1rfn 2wph 2wpi 2wpj 2wpk 2wpl 2wpm 3kcg 3lc3 3lc5 4wm0 4wma 4wmb 4wmi 4wmk 4wn2 4wnh 4yzu 4z0k 4zae 5egm 5f84 5f86 5jb8 5jb9 5jba 5jbb 5jbc 5tno 5tnt
        RUMI_DROME | Q8T045: 5f84 5f86 5f87

(-) Related Entries Specified in the PDB File

5f84 5f86 5f87