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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE XYLOSIDE XYLOSYLTRANSFERASE 1 COMPLEXED WITH MANGANESE, PRODUCT LIGAND AND UDP (PRODUCT COMPLEX II)
 
Authors :  H. Yu, H. Li
Date :  09 Oct 14  (Deposition) - 30 Sep 15  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Glycosyltransferase, Transferase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yu, M. Takeuchi, J. Lebarron, J. Kantharia, E. London, H. Bakker, R. S. Haltiwanger, H. Li, H. Takeuchi
Notch-Modifying Xylosyltransferase Structures Support An Sni-Like Retaining Mechanism.
Nat. Chem. Biol. V. 11 847 2015
PubMed-ID: 26414444  |  Reference-DOI: 10.1038/NCHEMBIO.1927

(-) Compounds

Molecule 1 - XYLOSIDE XYLOSYLTRANSFERASE 1
    Chains: A
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 87-392
    Gene: XXYLT1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - COAGULATION FACTOR IX
    Chains: D
    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 : AD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1GXX1Ligand/IonALPHA-D-XYLOPYRANOSYL-(1->3)-ALPHA-D-XYLOPYRANOSYL-(1->3)-BETA-D-GLUCOPYRANOSE
2MN1Ligand/IonMANGANESE (II) ION
3SO41Ligand/IonSULFATE ION
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:225 , ASP A:227 , HIS A:382 , UDP A:402binding site for residue MN A 401
2AC2SOFTWAREMET A:103 , PHE A:104 , THR A:105 , LEU A:113 , LYS A:116 , ASP A:225 , LEU A:226 , ASP A:227 , HIS A:382 , ASN A:384 , CYS A:385 , MN A:401 , HOH A:578 , GXX D:101binding site for residue UDP A 402
3AC3SOFTWAREARG A:254 , HIS A:269 , ASP A:348 , CYS A:349 , HOH A:512 , HOH A:540binding site for residue SO4 A 403
4AC4SOFTWAREASP A:225 , GLU A:255 , GLN A:257 , VAL A:259 , ASN A:288 , SER A:289 , GLY A:290 , GLN A:330 , TRP A:358 , TRP A:359 , HIS A:382 , ASN A:384 , CYS A:385 , UDP A:402 , SER D:53 , HOH D:202 , HOH D:204 , HOH D:207binding site for residue GXX D 101

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:349 -A:374
2A:356 -A:385
3D:51 -D:62
4D:56 -D:71
5D:73 -D:82

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:158 -Pro A:159
2Ala A:193 -Gly A:194
3Ser A:195 -Gly A:196
4Pro A:280 -Pro A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WMK)

(-) 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:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhhhhhhhhhhhh.....eeeeeeeeehhhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhh.....eeeee...eee..hhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh...............eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeehhhhhee..hhhhhhhhhhhhhhhhh......eee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wmk A  93 VVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEASREVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIPE 391
                                   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 D from PDB  Type:PROTEIN  Length:35
                                                                   
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 4wmk D  50 QCESNPCLNGGSCKDDINSYECWCPFGFEGKNCEL  84
                                    59        69        79
   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 4WMK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:193 - Gly A:194   [ RasMol ]  
    Leu A:158 - Pro A:159   [ RasMol ]  
    Pro A:280 - Pro A:281   [ RasMol ]  
    Ser A:195 - Gly A:196   [ RasMol ]  
 

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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 4wn2 4wnh 4yzu 4z0k 4zae 5egm 5f84 5f85 5f86 5jb8 5jb9 5jba 5jbb 5jbc 5tno 5tnt
        XXLT1_MOUSE | Q3U4G3: 4wlg 4wlm 4wlz 4wm0 4wma 4wmb 4wmi 4wn2 4wnh

(-) Related Entries Specified in the PDB File

4wlg 4wlm 4wlz 4wm0 4wma 4wmb 4wmi 4wn2