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(-) Description

Title :  HUMAN OGT IN COMPLEX WITH UDP-5S-GLCNAC AND SUBSTRATE PEPTIDE (RB2L)
 
Authors :  M. Schimpl, K. Rafie, D. M. F. Van Aalten
Date :  13 Jun 15  (Deposition) - 05 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,C
Keywords :  O-Glcnac Transferase Inverting Gt-B Substrate Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pathak, J. Alonso, M. Schimpl, K. Rafie, D. E. Blair, V. S. Borodkin, A. W. Schuttelkopf, O. Albarbarawi, D. M. Van Aalten
The Active Site Of O-Glcnac Transferase Imposes Constraints On Substrate Sequence.
Nat. Struct. Mol. Biol. V. 22 744 2015
PubMed-ID: 26237509  |  Reference-DOI: 10.1038/NSMB.3063

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N- ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT
    Chains: A
    EC Number: 2.4.1.255
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Fragment: UNP RESIDUES 313-1031
    Gene: OGT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: O-GLCNAC TRANSFERASE, O-GLCNAC TRANSFERASE SUBUNIT P110,O- LINKED N-ACETYLGLUCOSAMINE TRANSFERASE 110 KDA SUBUNIT,OGT
 
Molecule 2 - RETINOBLASTOMA-LIKE PROTEIN 2
    Chains: C
    Engineered: YES
    Fragment: UNP RESIDUES 416-423
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: NITROGEN FROM RESIDUE 8 RESULTS FROM AN ACETYLATION DURING CHEMICAL SYNTHESIS OF THE COMPOUND AND IS PART OF RESIDUE 7 BUT NEEDED A DIFFERENT RESIDUE NUMBER IN THE PDB
    Synonym: 130 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN,P130, RETINOBLASTOMA-RELATED PROTEIN 2,RBR-2,PRB2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
112V1Ligand/Ion(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:498 , PRO A:559 , THR A:560 , LEU A:653 , GLY A:654 , PRO A:656 , PHE A:694 , GLN A:839 , TYR A:841 , LYS A:842 , LEU A:866 , VAL A:895 , ALA A:896 , LYS A:898 , HIS A:901 , ARG A:904 , HIS A:920 , THR A:921 , THR A:922 , ASP A:925 , HOH A:1267 , HOH A:1283 , HOH A:1284 , HOH A:1325 , HOH A:1336 , PRO C:3 , VAL C:4 , SER C:5binding site for residue 12V A 1101
2AC2SOFTWARELEU A:405 , HIS A:429 , SER A:432 , ASN A:434binding site for residue PO4 A 1102
3AC3SOFTWAREGLN A:413 , PRO A:436 , ILE A:439 , VAL A:871 , ASN A:875 , HOH A:1358binding site for residue PO4 A 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C1D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:868 -Pro A:869

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C1D)

(-) Exons   (0, 0)

(no "Exon" information available for 5C1D)

(-) 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:695
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..................eeeeeee.....hhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhh.eeee.hhh.hhhhhhhhhhhhh..eeee.........hhhhhh....eeee..............eeee.....hhhhhhhh..eeee........hhhhhhhhhh..eeee........eeee..hhhhhhhh....eee....eeeee.hhhhhhhhhhhhh...eeee..eeeee..hhhhhhhhhhh.......eeeee.hhhh......eee...hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...hhh.eeeee..hhhhhhhhhhhh.eee.......hhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c1d A  315 THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSIYDNRIVLNGIDLKAFLDSLPDVKIVKMLNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMI 1027
                                   324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714||     727       737       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022     
                                                                                                                                                                                                                                                                                                                                                                                                                                          715|                        746|                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                           719                         762                                                                                                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:8
                                         
               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
                5c1d C    1 VTPVSTAA    8
   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 5C1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C1D)

(-) Gene Ontology  (87, 91)

Asymmetric/Biological Unit(hide GO term definitions)

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    Phe A:868 - Pro A:869   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        OGT1_HUMAN | O15294: 1w3b 3pe3 3pe4 3tax 4ay5 4ay6 4cdr 4gyw 4gyy 4gz3 4gz5 4gz6 4n39 4n3a 4n3b 4n3c 4xi9 4xif 5bnw 5hgv 5lvv 5lwv
        RBL2_HUMAN | Q08999: 4xi9

(-) Related Entries Specified in the PDB File

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