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 HUMAN PRIMPOL TERNARY COMPLEX
 
Authors :  O. Rechkoblit, Y. K. Gupta, R. Malik, K. R. Rajashankar, R. E. Johnson, L S. Prakash, A. K. Aggarwal
Date :  02 Aug 16  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,G,H
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,G,H  (1x)
Keywords :  Protein-Dna Complex, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Rechkoblit, Y. K. Gupta, R. Malik, K. R. Rajashankar, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Structure And Mechanism Of Human Primpol, A Dna Polymerase With Primase Activity.
Sci Adv V. 2 01317 2016
PubMed-ID: 27819052  |  Reference-DOI: 10.1126/SCIADV.1601317

(-) Compounds

Molecule 1 - DNA-DIRECTED PRIMASE/POLYMERASE PROTEIN
    ChainsA, B
    EC Number2.7.7.-
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System Taxid4932
    GenePRIMPOL, CCDC111
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHPRIMPOL1,COILED-COIL DOMAIN-CONTAINING PROTEIN 111
 
Molecule 2 - DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')
    ChainsC, G
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES
 
Molecule 3 - DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')
    ChainsD, H
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDGH
Biological Unit 1 (1x)A CD  
Biological Unit 2 (1x) B  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
15IU2Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3DDG2Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
15IU1Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3DDG1Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
15IU1Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3DDG1Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:76 , TYR A:100 , ASP A:114 , GLU A:116 , LYS A:165 , SER A:167 , HIS A:169 , ARG A:288 , ASN A:289 , ARG A:291 , LYS A:297 , CA A:402 , HOH A:519 , HOH A:530 , DT C:3 , DDG D:14binding site for residue DTP A 401
2AC2SOFTWAREASP A:114 , GLU A:116 , DTP A:401 , HOH A:514binding site for residue CA A 402
3AC3SOFTWAREARG B:76 , TYR B:100 , ASP B:114 , GLU B:116 , LYS B:165 , SER B:167 , HIS B:169 , ARG B:288 , ASN B:289 , ARG B:291 , LYS B:297 , CA B:402 , HOH B:537 , HOH B:544 , DT G:3 , DDG H:14binding site for residue DTP B 401
4AC4SOFTWAREASP B:114 , GLU B:116 , DTP B:401 , HOH B:503binding site for residue CA B 402
5AC5SOFTWAREDG G:5 , DA G:8 , DT H:10 , DA H:11 , DG H:12binding site for Di-nucleotide DC G 6 and 5IU G 7
6AC6SOFTWAREDC G:6 , DC G:9 , DG H:9 , DT H:10 , DA H:11 , DG H:12binding site for Di-nucleotide 5IU G 7 and DA G 8
7AC7SOFTWAREASP B:280 , ARG B:288 , DTP B:401 , DC G:4 , DG G:5 , DG H:12binding site for Di-nucleotide DC H 13 and DDG H 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L2X)

(-) Exons   (0, 0)

(no "Exon" information available for 5L2X)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhh.....eeeeee.......eeeeeehhhhhhhhhh.......eeee.........eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee.....eeeeeeee....eee.hhhhhhhhhhhhhhhhhhh...hhh.eee.....eee..hhhhh....eee.............ee..............hhhhhhhhhhh..........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l2x A   1 MNRKWEAKLKQIEERASPEEPPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEP 348
                                    10      ||37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197  ||   267       277       287       297       307       317       327       337       347 
                                           17|                                                                                                                                                                  200|                                                                                       
                                            35                                                                                                                                                                   261                                                                                       

Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhhhhhh.......eeeee........eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee.....eeeeeeee....eee.hhhhhhhhhhhhhhhhhh....hhh.eee.....eee..hhhhh...eeee.............ee..............hhhhhhhhhhh..........eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l2x B  38 PPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEP 348
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197  ||   267       277       287       297       307       317       327       337       347 
                                                                                                                                                                                            200|                                                                                       
                                                                                                                                                                                             261                                                                                       

Chain C from PDB  Type:DNA  Length:12
                                            
                 5l2x C   2 ATCGCuACCACA  13
                                 |  11  
                                 7-5IU  

Chain D from PDB  Type:DNA  Length:7
                                       
                 5l2x D   8 GGTAGCx  14
                                  |
                                 14-DDG

Chain G from PDB  Type:DNA  Length:8
                                        
                 5l2x G   3 TCGCuACC  10
                                |   
                                |   
                                7-5IU

Chain H from PDB  Type:DNA  Length:7
                                       
                 5l2x H   8 GGTAGCx  14
                                  |
                                 14-DDG

   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 5L2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L2X)

(-) Gene Ontology  (20, 20)

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
    5IU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DDG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTP  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5l2x)
 
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
  5l2x
    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
  PRIPO_HUMAN | Q96LW4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.-
    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
  PRIPO_HUMAN | Q96LW4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRIPO_HUMAN | Q96LW45n85 5n8a

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L2X)