Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1 IN COMPLEX WITH 8-OXO-DGTP, 8-OXO-DGMP AND PYROPHOSPHATE (II)
 
Authors :  S. M. Arif, A. G. Patil, U. Varshney, M. Vijayan
Date :  15 Jun 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  8-Oxo-Guanine Nucleotides, Sanitization Of Nucleotide Pool, Nudix Enzyme, Histidine Phosphatase Domain, Binding Sites At Intermolecular Interface, Enzyme Action, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Arif, A. G. Patil, U. Varshney, M. Vijayan
Biochemical And Structural Studies Of Mycobacterium Smegmatis Mutt1, A Sanitization Enzyme With Unusual Modes O Association
Acta Crystallogr D Struct V. 73 349 2017 Biol
PubMed-ID: 28375146  |  Reference-DOI: 10.1107/S2059798317002534
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROLASE, NUDIX FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JW0097
    Expression System Taxid: 562
    Gene: MSMEG_2390
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: MC2 155
    Synonym: MUTT1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
18DG1Ligand/Ion8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
28OG1Ligand/Ion8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:55 , TYR A:58 , SER A:62 , LYS A:65 , LYS A:67 , TYR A:101 , LYS A:108 , TYR A:145 , MG A:404 , HOH A:509 , HOH A:536 , HOH A:553 , HOH A:559 , HOH A:563 , HOH A:572 , HOH A:585 , HOH A:617 , HOH A:638 , HOH A:648 , HOH A:664binding site for residue 8DG A 401
2AC2SOFTWAREASP A:59 , TRP A:61 , ASP A:141 , GLN A:142 , GLN A:144 , HOH A:526 , HOH A:650 , HOH A:673 , HOH A:686binding site for residue 8OG A 402
3AC3SOFTWAREARG A:169 , HIS A:170 , ARG A:176 , ARG A:186 , ARG A:218 , GLN A:271 , GLY A:272 , LYS A:297 , HOH A:518 , HOH A:520 , HOH A:545 , HOH A:549binding site for residue POP A 403
4AC4SOFTWARELYS A:65 , GLU A:85 , 8DG A:401 , HOH A:603 , HOH A:615 , HOH A:664binding site for residue MG A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GG8)

(-) Exons   (0, 0)

(no "Exon" information available for 5GG8)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee......eeeeeee....eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeeee..eeeeeeeeeeeeeee.........eeeeeehhhhhhhh.hhhhhhhhhhhhhh....eeeeeee...................hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh.............eeeeeee..eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gg8 A  21 KHTVRAAGAVLWRDAPATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK 322
                                    30    ||  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   
                                         35|                                                                                                                                                                                                                                                                                     
                                          45
   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 5GG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GG8)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    8DG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    8OG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    POP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gg8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5gg8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A0QUZ2_MYCS2 | A0QUZ2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A0QUZ2_MYCS2 | A0QUZ2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0QUZ2_MYCS2 | A0QUZ2: 5gg5 5gg6 5gg7 5gg9 5gga 5ggb 5ggc 5ggd

(-) Related Entries Specified in the PDB File

5gg5 5gg6 5gg7 5gg9 5gga 5ggb 5ggc 5ggd