Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF DR2231_E47A MUTANT IN COMPLEX WITH DUMP AND MANGANESE
 
Authors :  C. S. Mota, A. M. D. Goncalves, D. De Sanctis
Date :  03 Feb 16  (Deposition) - 26 Oct 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Alpha Helix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. S. Mota, A. M. Goncalves, D. De Sanctis
Deinococcus Radiodurans Dr2231 Is A Two-Metal-Ion Mechanism Hydrolase With Exclusive Activity On Dutp.
Febs J. V. 283 4274 2016
PubMed-ID: 27739259  |  Reference-DOI: 10.1111/FEBS.13923

(-) Compounds

Molecule 1 - DR2231
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET151/D-TOPO
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneDR_2231
    Organism ScientificDEINOCOCCUS RADIODURANS (STRAIN ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
    Organism Taxid243230

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION
2UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:50 , GLU A:79 , ASP A:82 , HOH A:315 , HOH A:414 , HOH A:418binding site for residue MN A 201
2AC2SOFTWAREGLU B:79 , ASP B:82 , HOH B:952 , HOH B:1007 , HOH B:1035 , HOH B:1045binding site for residue MN B 201
3AC3SOFTWAREASN A:109 , LYS A:112 , LYS A:122 , GLN A:123 , LYS A:125 , PHE C:17 , GLU C:46 , ASP C:82 , TYR C:85 , VAL C:86 , MN C:202 , HOH C:322 , HOH C:330 , HOH C:339 , HOH C:371 , HOH C:372 , HOH C:385 , HOH C:434binding site for residue UMP C 201
4AC4SOFTWAREGLU C:46 , GLU C:50 , UMP C:201 , HOH C:385 , HOH C:401 , HOH C:434binding site for residue MN C 202
5AC5SOFTWAREGLU C:50 , GLU C:79 , ASP C:82 , HOH C:383 , HOH C:385 , HOH C:401binding site for residue MN C 203
6AC6SOFTWAREASN B:109 , LYS B:112 , LYS B:122 , GLN B:123 , LYS B:125 , PHE D:17 , GLU D:46 , ASP D:82 , TYR D:85 , VAL D:86 , MN D:202 , HOH D:331 , HOH D:333 , HOH D:342 , HOH D:352 , HOH D:364 , HOH D:366 , HOH D:406binding site for residue UMP D 201
7AC7SOFTWAREGLU D:46 , GLU D:50 , UMP D:201 , MN D:203 , HOH D:366 , HOH D:396 , HOH D:427binding site for residue MN D 202
8AC8SOFTWAREGLU D:50 , GLU D:79 , ASP D:82 , MN D:202 , HOH D:363 , HOH D:366 , HOH D:396binding site for residue MN D 203

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:6 -D:6

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HZZ)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....................hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hzz A   7 PPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEASAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHA 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        

Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hzz B   6 CPPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEASAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHA 144
                                    15        25        35        45        55        65        75        85        95       105       115       125       135         

Chain C from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hzz C  -4 IDPFTMSDLPCPPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEASAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGLKPEGWRPADVRGVIERLQHA 144
                                     5        15        25        35        45        55        65        75        85        95       105       115|      133       143 
                                                                                                                                                 115|                    
                                                                                                                                                  124                    

Chain D from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hzz D  -4 IDPFTMSDLPCPPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEASAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGLKPEGWRPADVRGVIERLQHA 144
                                     5        15        25        35        45        55        65        75        85        95       105       115|      133       143 
                                                                                                                                                 115|                    
                                                                                                                                                  124                    

   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 5HZZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5hzz)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5hzz
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9RS96_DEIRA | Q9RS96
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q9RS96_DEIRA | Q9RS96
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9RS96_DEIRA | Q9RS962yeu 2yf3 2yf4 2yf9 2yfc 2yfd 5hva 5hwu 5hx1 5hyl 5i0j 5i0m

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HZZ)