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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SAUGI/HUMAN UDG COMPLEX
 
Authors :  H. C. Wang, T. P. Ko, M. F. Huang, A. H. J. Wang
Date :  02 Sep 15  (Deposition) - 08 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna Mimic Protein, Dna Mimicking, Uracil-Dna Glycosylase Inhibitor, Uracil-Dna Glycosylase, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. C. Wang, C. H. Ho, C. C. Chou, T. P. Ko, M. F. Huang, K. C. Hsu, A. H. Wang
Using Structural-Based Protein Engineering To Modulate The Differential Inhibition Effects Of Saugi On Human And Hsv Uracil Dna Glycosylase.
Nucleic Acids Res. V. 44 4440 2016
PubMed-ID: 26980279  |  Reference-DOI: 10.1093/NAR/GKW185

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    ChainsA, C
    EC Number3.2.2.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 94-313
    GeneUNG, DGU, UNG1, UNG15
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUDG
 
Molecule 2 - UNCHARACTERIZED PROTEIN
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid1280
    SynonymSAUGI

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:145 , ASN A:215 , HOH A:1006 , HOH A:1009 , HOH A:1071 , HOH B:1008binding site for residue MG A 900
2AC2SOFTWAREASP B:88 , MET B:89 , HOH B:1015 , HOH B:1027 , ASP D:88 , MG D:900binding site for residue MG B 900
3AC3SOFTWAREASP C:145 , ASN C:215 , HOH C:1007 , HOH C:1009 , HOH C:1029 , HOH C:1071binding site for residue MG C 900
4AC4SOFTWAREASP B:88 , MG B:900 , HOH B:1015 , ASP D:88 , MET D:89 , HOH D:1007binding site for residue MG D 900

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:119 -Pro A:120
2Arg A:162 -Pro A:163
3Tyr C:119 -Pro C:120
4Arg C:162 -Pro C:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AYR)

(-) Sequences/Alignments

Asymmetric 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhh....eeeeehhhhhhhh........eeeee......hhhhh....hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayr A  82 MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKELL 305
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    

Chain B from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......eeeeeeee.hhh.hhhhh........eeeeeeeehhhhhhhh.eeeeeee..eeeeeeee.....eeeeeee....eeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5ayr B   1 MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDTLHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLT 109
                                    10        20        30        40        50        60        70        80        90       100         

Chain C from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhh....eeeeehhhhhhhh........eeeee......hhhhh....hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayr C  82 MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKELL 305
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    

Chain D from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......eeeeeeee.hhh.hhhhh........eeeeeeeehhhhhhhh.eeeeeee..eeeeeeee.....eeeeeee....eeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5ayr D   1 MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDTLHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLT 109
                                    10        20        30        40        50        60        70        80        90       100         

   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 5AYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_HUMAN | P130511akz 1dpu 1emh 1emj 1q3f 1ssp 1ugh 1yuo 2hxm 2oxm 2oyt 2ssp 3fcf 3fci 3fck 3fcl 3tkb 4skn 5jk7
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        Q936H5_STAAU | Q936H53wdg 5ays

(-) Related Entries Specified in the PDB File

5ays